

In [1]:

    
%%bq query
#standardSQL
  --
  -- Return variants for sample NA12878 that are:
  --   annotated as 'pathogenic' or 'other' in ClinVar
  --   with observed population frequency less than 5%
  --
  WITH sample_variants AS (
  SELECT
    -- Remove the 'chr' prefix from the reference name.
    REGEXP_EXTRACT(reference_name, r'chr(.+)') AS chr,
    start,
    reference_bases,
    alt,
    call.call_set_name
  FROM
    `genomics-public-data.platinum_genomes_deepvariant.single_sample_genome_calls` v,
    v.call call,
    v.alternate_bases alt WITH OFFSET alt_offset
  WHERE
    call_set_name = 'NA12878_ERR194147'
    -- Require that at least one genotype matches this alternate.
    AND EXISTS (SELECT gt FROM UNNEST(call.genotype) gt WHERE gt = alt_offset+1)
    ),
  --
  --
  rare_pathenogenic_variants AS (
  SELECT
    -- ClinVar does not use the 'chr' prefix for reference names.
    reference_name AS chr,
    start,
    reference_bases,
    alt,
    CLNHGVS,
    CLNALLE,
    CLNSRC,
    CLNORIGIN,
    CLNSRCID,
    CLNSIG,
    CLNDSDB,
    CLNDSDBID,
    CLNDBN,
    CLNREVSTAT,
    CLNACC
  FROM
    `bigquery-public-data.human_variant_annotation.ncbi_clinvar_hg38_20170705` v,
    v.alternate_bases alt
  WHERE
    -- Variant Clinical Significance, 0 - Uncertain significance, 1 - not provided,
    -- 2 - Benign, 3 - Likely benign, 4 - Likely pathogenic, 5 - Pathogenic,
    -- 6 - drug response, 7 - histocompatibility, 255 - other
    EXISTS (SELECT sig FROM UNNEST(CLNSIG) sig WHERE REGEXP_CONTAINS(sig, '(4|5|255)'))
    -- TRUE if >5% minor allele frequency in 1+ populations
    AND G5 IS NULL
)
 --
 --
SELECT
  *
FROM
  sample_variants
JOIN
  rare_pathenogenic_variants USING(chr,
    start,
    reference_bases,
    alt)
ORDER BY
  chr,
  start,
  reference_bases,
  alt









    Out[1]:





    chr start reference_bases alt call_set_name CLNHGVS CLNALLE CLNSRC CLNORIGIN CLNSRCID CLNSIG CLNDSDB CLNDSDBID CLNDBN CLNREVSTAT CLNACC
1 94047008 C T NA12878_ERR194147 ['NC_000001.11:g.94047009C>T'] [2] ['HGMD|OMIM_Allelic_Variant|UniProtKB_(protein)'] [1] ['CM024629|601691.0035|P78363#VAR_008428'] ['255|5|1|2|3|3|3|3'] ['MedGen:OMIM|MedGen|MedGen|Human_Phenotype_Ontology:MedGen|MedGen|MedGen|MedGen'] ['C1855465:248200|CN221809|CN169374|HP:0000608:C0024437|CN239309|CN239466|CN239312'] ['MACULAR_DEGENERATION\\x2c_AGE-RELATED\\x2c_2\\x2c_SUSCEPTIBILITY_TO|Stargardt_disease_1|not_provided|not_specified|Macular_degeneration|Cone-Rod_Dystrophy\\x2c_Recessive|Retinitis_Pigmentosa\\x2c_Recessive|Stargardt_Disease\\x2c_Recessive'] ['no_criteria|no_criteria|no_assertion|mult|single|single|single|single'] ['RCV000008374.4|RCV000008375.4|RCV000085512.3|RCV000152706.4|RCV000294335.1|RCV000349295.1|RCV000392936.1|RCV000399411.1']
1 201361939 A G NA12878_ERR194147 ['NC_000001.11:g.201361940A>G'] [1] ['.'] [1] ['.'] ['255|0|0|0|0|0|0|0'] ['MedGen|MedGen:OMIM|MedGen:OMIM|MedGen:OMIM|Human_Phenotype_Ontology:MedGen|Human_Phenotype_Ontology:MedGen:Orphanet|MedGen|MedGen:Orphanet:SNOMED_CT'] ['CN169374|C1861864:115195|C2676271:612422|C1832243:601494|HP:0011664:C4021133|HP:0001639:C0007194:ORPHA217569|CN239310|C0340429:ORPHA217635:233878008'] ['not_specified|Familial_hypertrophic_cardiomyopathy_2|Familial_restrictive_cardiomyopathy_3|Left_ventricular_noncompaction_6|Left_ventricular_noncompaction_cardiomyopathy|Hypertrophic_cardiomyopathy|Dilated_Cardiomyopathy\\x2c_Dominant|Familial_restrictive_cardiomyopathy'] ['conf|single|single|single|single|single|single|single'] ['RCV000168973.2|RCV000230425.2|RCV000230425.2|RCV000230425.2|RCV000283636.1|RCV000323526.1|RCV000338870.1|RCV000378147.1']
1 212897348 T TACAC NA12878_ERR194147 ['NC_000001.11:g.212897351_212897370dup20', 'NC_000001.11:g.212897365_212897370dupCACACA', 'NC_000001.11:g.212897367_212897370dupCACA', 'NC_000001.11:g.212897369_212897370dupCA'] [4, -1, -1, -1] ['.', '.', '.', '.'] [1, 1, 1, 1] ['.', '.', '.', '.'] ['0', '3', '255', '0'] ['MedGen:OMIM:Orphanet', 'MedGen:OMIM:Orphanet', 'MedGen:OMIM:Orphanet', 'MedGen:OMIM:Orphanet'] ['C1836916:609033:ORPHA88628', 'C1836916:609033:ORPHA88628', 'C1836916:609033:ORPHA88628', 'C1836916:609033:ORPHA88628'] ['Posterior_column_ataxia_with_retinitis_pigmentosa', 'Posterior_column_ataxia_with_retinitis_pigmentosa', 'Posterior_column_ataxia_with_retinitis_pigmentosa', 'Posterior_column_ataxia_with_retinitis_pigmentosa'] ['single', 'single', 'conf', 'single'] ['RCV000355025.1', 'RCV000297866.1', 'RCV000262602.1', 'RCV000351203.1']
1 215671030 C T NA12878_ERR194147 ['NC_000001.11:g.215671031C>T'] [1] ['UniProtKB_(protein)'] [1] ['O75445#VAR_061351'] ['255'] ['MedGen'] ['CN169374'] ['not_specified'] ['conf'] ['RCV000041750.4']
1 237589773 AT A NA12878_ERR194147 ['NC_000001.11:g.237589784delT'] [1] ['.'] [1] ['.'] ['2|255'] ['MedGen:Orphanet:SNOMED_CT|MedGen'] ['C0878544:ORPHA167848:85898001|CN169374'] ['Cardiomyopathy|not_specified'] ['no_criteria|conf'] ['RCV000030420.1|RCV000036734.8']
10 26088401 C T NA12878_ERR194147 ['NC_000010.11:g.26088402C>T'] [1] ['.'] [1] ['.'] ['255|0'] ['MedGen|MedGen'] ['CN169374|CN239439'] ['not_specified|Nonsyndromic_Hearing_Loss\\x2c_Recessive'] ['conf|single'] ['RCV000039026.3|RCV000381484.1']
11 6392135 C T NA12878_ERR194147 ['NC_000011.10:g.6392136C>T'] [1] ['.'] [1] ['.'] ['255|0'] ['MedGen|MedGen:SNOMED_CT'] ['CN169374|C0028064:58459009'] ['not_specified|Sphingomyelin/cholesterol_lipidosis'] ['conf|single'] ['RCV000079188.5|RCV000394529.1']
11 6617153 C T NA12878_ERR194147 ['NC_000011.10:g.6617154C>A', 'NC_000011.10:g.6617154C>G', 'NC_000011.10:g.6617154C>T'] [1, 2, 3] ['.', 'OMIM_Allelic_Variant', '.'] [1, 1, 1] ['.', '607998.0004', '.'] ['5', '5|5|5|5|5', '5'] ['MedGen', 'MedGen:OMIM:Orphanet|MedGen:OMIM:Orphanet|MedGen|MeSH:MedGen|MedGen:OMIM:Orphanet:SNOMED_CT', 'MedGen'] ['CN221809', 'C1876161:204500:ORPHA228349|C1836474:609270:ORPHA284324|CN221809|D030342:C0950123|C0027877:214200:ORPHA216:42012007', 'CN221809'] ['not_provided', 'Ceroid_lipofuscinosis_neuronal_2|Childhood-onset_autosomal_recessive_slowly_progressive_spinocerebellar_ataxia|not_provided|Inborn_genetic_diseases|Neuronal_ceroid_lipofuscinosis', 'not_provided'] ['single', 'mult|single|mult|single|single', 'single'] ['RCV000391641.1', 'RCV000002763.11|RCV000074608.7|RCV000189765.4|RCV000210689.1|RCV000228119.2', 'RCV000189764.3']
11 47448802 C T NA12878_ERR194147 ['NC_000011.10:g.47448803C>T'] [1] ['.'] [1] ['.'] ['255'] ['MedGen'] ['CN169374'] ['not_specified'] ['conf'] ['RCV000246056.2']
11 66510682 T C NA12878_ERR194147 ['NC_000011.10:g.66510683T>C'] [1] ['.'] [1] ['.'] ['255|2'] ['MedGen|MedGen:OMIM:Orphanet:SNOMED_CT'] ['CN169374|C0752166:209900:ORPHA110:5619004'] ['not_specified|Bardet-Biedl_syndrome'] ['conf|single'] ['RCV000173529.2|RCV000226235.1']
12 102840473 T C NA12878_ERR194147 ['NC_000012.12:g.102840474T>C'] [1] ['HGMD|OMIM_Allelic_Variant|UniProtKB_(protein)'] [1] ['CM910294|612349.0017|P00439#VAR_001038'] ['5|5|5'] ['MedGen|MedGen|MedGen:OMIM:Orphanet:SNOMED_CT'] ['C0751435|CN221809|C0031485:261600:ORPHA716:154735006'] ['Hyperphenylalaninemia\\x2c_non-pku|not_provided|Phenylketonuria'] ['no_criteria|single|mult'] ['RCV000000624.4|RCV000078508.6|RCV000150074.4']
14 23389061 AG A NA12878_ERR194147 ['NC_000014.9:g.23389063delG'] [1] ['.'] [1] ['.'] ['3|255|2|0|0|0'] ['MedGen:Orphanet:SNOMED_CT|MedGen|MedGen:OMIM|MedGen:Orphanet|MedGen|Human_Phenotype_Ontology:MedGen:Orphanet'] ['C0878544:ORPHA167848:85898001|CN169374|C2750467:613251|C0018817:ORPHA1478|CN239310|HP:0001639:C0007194:ORPHA217569'] ['Cardiomyopathy|not_specified|Familial_hypertrophic_cardiomyopathy_14|Atrial_septal_defect|Dilated_Cardiomyopathy\\x2c_Dominant|Hypertrophic_cardiomyopathy'] ['single|conf|single|single|single|single'] ['RCV000030306.1|RCV000154759.3|RCV000205051.2|RCV000299696.1|RCV000354591.1|RCV000396023.1']
14 64210032 C T NA12878_ERR194147 ['NC_000014.9:g.64210033C>T'] [2] ['OMIM_Allelic_Variant|UniProtKB_(protein)'] [1] ['608442.0001|Q8WXH0#VAR_062977'] ['5|255|3'] ['MedGen:OMIM|MedGen|MedGen:Orphanet:SNOMED_CT'] ['C2751805:612999|CN169374|C0410189:ORPHA261:111508004'] ['Emery-Dreifuss_muscular_dystrophy_5\\x2c_autosomal_dominant|not_specified|Emery-Dreifuss_muscular_dystrophy'] ['no_criteria|conf|single'] ['RCV000002414.4|RCV000173937.3|RCV000403391.1']
15 65078011 C T NA12878_ERR194147 ['NC_000015.10:g.65078012C>T'] [1] ['.'] [1] ['.'] ['255|3'] ['MedGen|MedGen'] ['CN169374|CN239448'] ['not_specified|Nemaline_Myopathy\\x2c_Dominant'] ['conf|single'] ['RCV000117307.4|RCV000304321.1']
15 89645160 A T NA12878_ERR194147 ['NC_000015.10:g.89645161A>T'] [1] ['.'] [1] ['.'] ['255|3'] ['MedGen|Gene:MedGen:OMIM:Orphanet'] ['CN169374|46:C0796147:200990:ORPHA36'] ['not_specified|Acrocallosal_syndrome\\x2c_Schinzel_type'] ['conf|single'] ['RCV000117416.4|RCV000261344.1']
16 2497032 C G NA12878_ERR194147 ['NC_000016.10:g.2497033C>G'] [1] ['UniProtKB_(protein)'] [1] ['Q9ULP9#VAR_070890'] ['255|3|3|3'] ['MedGen|MedGen|MedGen:OMIM|MedGen:OMIM'] ['CN169374|C3809181|C3892048:616044|C3463992:308350'] ['not_specified|Caused_by_mutation_in_the_TBC1_domain_family\\x2c_member_24|Deafness\\x2c_autosomal_dominant_65|Epileptic_encephalopathy\\x2c_early_infantile\\x2c_1'] ['conf|single|single|single'] ['RCV000128367.6|RCV000477643.1|RCV000477643.1|RCV000477643.1']
16 56514588 C T NA12878_ERR194147 ['NC_000016.10:g.56514589C\\x3d', 'NC_000016.10:g.56514589C>T'] [0, 1] ['OMIM_Allelic_Variant', '.'] [1, 1] ['606151.0013', '.'] ['5', '2'] ['MedGen', 'MedGen'] ['C4016908', 'CN169374'] ['Bardet-biedl_syndrome_2/6\\x2c_digenic', 'not_specified'] ['no_criteria', 'single'] ['RCV000004838.4', 'RCV000301991.1']
16 88805736 T C NA12878_ERR194147 ['NC_000016.10:g.88805737T>C'] [1] ['UniProtKB_(protein)'] [1] ['Q9H211#VAR_054504'] ['255'] ['MedGen'] ['CN169374'] ['not_specified'] ['conf'] ['RCV000116652.3']
17 17796722 AAGG A NA12878_ERR194147 ['NC_000017.11:g.17796729_17796731delGAG'] [1] ['HGMD'] [1] ['CD116392'] ['255|0'] ['MedGen|MedGen'] ['CN169374|CN221809'] ['not_specified|not_provided'] ['conf|single'] ['RCV000082265.6|RCV000118114.3']
18 2700878 A G NA12878_ERR194147 ['NC_000018.10:g.2700879A>G'] [1] ['.'] [1] ['.'] ['255'] ['MedGen'] ['CN169374'] ['not_specified'] ['conf'] ['RCV000247697.2']
19 11132530 C CA NA12878_ERR194147 ['NC_000019.10:g.11125285_11132532dup7248', 'NC_000019.10:g.11132532dupA'] [-1, 1] ['LDLR_@_LOVD', '.'] [5, 1] ['LDLR_000294', '.'] ['255', '3'] ['MedGen:OMIM:SNOMED_CT:SNOMED_CT', 'MedGen:OMIM:SNOMED_CT:SNOMED_CT'] ['C0020445:143890:397915002:398036000', 'C0020445:143890:397915002:398036000'] ['Familial_hypercholesterolemia', 'Familial_hypercholesterolemia'] ['conf', 'single'] ['RCV000237281.1', 'RCV000326993.1']
19 41414124 C T NA12878_ERR194147 ['NC_000019.10:g.41414125C>T'] [1] ['HGMD|UniProtKB_(protein)'] [1] ['CM021497|P12694#VAR_034361'] ['255|3'] ['MedGen|MedGen:OMIM:Orphanet:SNOMED_CT'] ['CN169374|C0024776:248600:ORPHA268184:27718001'] ['not_specified|Maple_syrup_urine_disease'] ['conf|single'] ['RCV000079243.6|RCV000295914.1']
19 45179661 C T NA12878_ERR194147 ['NC_000019.10:g.45179662C>T'] [1] ['.'] [1] ['.'] ['255|0'] ['MedGen|MedGen:SNOMED_CT'] ['CN169374|C0079504:9311003'] ['not_specified|Hermansky-Pudlak_syndrome'] ['conf|single'] ['RCV000150192.3|RCV000320201.1']
19 57231145 G GC NA12878_ERR194147 ['NC_000019.10:g.57231150dupC'] [1] ['.'] [1] ['.'] ['255'] ['MedGen'] ['CN239485'] ['Spermatogenic_Failure'] ['conf'] ['RCV000311416.1']
2 178532038 C T NA12878_ERR194147 ['NC_000002.12:g.178532039C>T'] [1] ['.'] [1] ['.'] ['255|2|2|2|3|3|3|3|3|3'] ['MedGen|MedGen:OMIM|MedGen:OMIM:Orphanet|MedGen|MedGen:OMIM:Orphanet|MedGen|Human_Phenotype_Ontology:MedGen:Orphanet|MedGen|MedGen:OMIM:Orphanet|MedGen:OMIM:Orphanet'] ['CN169374|C1858763:604145|C1837342:608807:ORPHA140922|CN230736|C2673677:611705:ORPHA289377|CN239352|HP:0001639:C0007194:ORPHA217569|CN239310|C1863599:603689:ORPHA178464|C1838244:600334:ORPHA609'] ['not_specified|Dilated_cardiomyopathy_1G|Limb-girdle_muscular_dystrophy\\x2c_type_2J|Cardiovascular_phenotype|Myopathy\\x2c_early-onset\\x2c_with_fatal_cardiomyopathy|Limb-Girdle_Muscular_Dystrophy\\x2c_Recessive|Hypertrophic_cardiomyopathy|Dilated_Cardiomyopathy\\x2c_Dominant|Hereditary_myopathy_with_early_respiratory_failure|Distal_myopathy_Markesbery-Griggs_type'] ['conf|single|single|single|single|single|single|single|single|single'] ['RCV000040944.8|RCV000231098.2|RCV000231098.2|RCV000244925.1|RCV000296735.1|RCV000311858.1|RCV000336579.1|RCV000351463.1|RCV000402951.1|RCV000403378.1']
    
(rows: 63, time: 5.0s,    10GB processed, job: job_P6NRU_M3B1MeX_TpuZdGC9QTWZwp)

chr	start	reference_bases	alt	call_set_name	CLNHGVS	CLNALLE	CLNSRC	CLNORIGIN	CLNSRCID	CLNSIG	CLNDSDB	CLNDSDBID	CLNDBN	CLNREVSTAT	CLNACC
1	94047008	C	T	NA12878_ERR194147	['NC_000001.11:g.94047009C>T']	[2]	['HGMD\|OMIM_Allelic_Variant\|UniProtKB_(protein)']	[1]	['CM024629\|601691.0035\|P78363#VAR_008428']	['255\|5\|1\|2\|3\|3\|3\|3']	['MedGen:OMIM\|MedGen\|MedGen\|Human_Phenotype_Ontology:MedGen\|MedGen\|MedGen\|MedGen']	['C1855465:248200\|CN221809\|CN169374\|HP:0000608:C0024437\|CN239309\|CN239466\|CN239312']	['MACULAR_DEGENERATION\\x2c_AGE-RELATED\\x2c_2\\x2c_SUSCEPTIBILITY_TO\|Stargardt_disease_1\|not_provided\|not_specified\|Macular_degeneration\|Cone-Rod_Dystrophy\\x2c_Recessive\|Retinitis_Pigmentosa\\x2c_Recessive\|Stargardt_Disease\\x2c_Recessive']	['no_criteria\|no_criteria\|no_assertion\|mult\|single\|single\|single\|single']	['RCV000008374.4\|RCV000008375.4\|RCV000085512.3\|RCV000152706.4\|RCV000294335.1\|RCV000349295.1\|RCV000392936.1\|RCV000399411.1']
1	201361939	A	G	NA12878_ERR194147	['NC_000001.11:g.201361940A>G']	[1]	['.']	[1]	['.']	['255\|0\|0\|0\|0\|0\|0\|0']	['MedGen\|MedGen:OMIM\|MedGen:OMIM\|MedGen:OMIM\|Human_Phenotype_Ontology:MedGen\|Human_Phenotype_Ontology:MedGen:Orphanet\|MedGen\|MedGen:Orphanet:SNOMED_CT']	['CN169374\|C1861864:115195\|C2676271:612422\|C1832243:601494\|HP:0011664:C4021133\|HP:0001639:C0007194:ORPHA217569\|CN239310\|C0340429:ORPHA217635:233878008']	['not_specified\|Familial_hypertrophic_cardiomyopathy_2\|Familial_restrictive_cardiomyopathy_3\|Left_ventricular_noncompaction_6\|Left_ventricular_noncompaction_cardiomyopathy\|Hypertrophic_cardiomyopathy\|Dilated_Cardiomyopathy\\x2c_Dominant\|Familial_restrictive_cardiomyopathy']	['conf\|single\|single\|single\|single\|single\|single\|single']	['RCV000168973.2\|RCV000230425.2\|RCV000230425.2\|RCV000230425.2\|RCV000283636.1\|RCV000323526.1\|RCV000338870.1\|RCV000378147.1']
1	212897348	T	TACAC	NA12878_ERR194147	['NC_000001.11:g.212897351_212897370dup20', 'NC_000001.11:g.212897365_212897370dupCACACA', 'NC_000001.11:g.212897367_212897370dupCACA', 'NC_000001.11:g.212897369_212897370dupCA']	[4, -1, -1, -1]	['.', '.', '.', '.']	[1, 1, 1, 1]	['.', '.', '.', '.']	['0', '3', '255', '0']	['MedGen:OMIM:Orphanet', 'MedGen:OMIM:Orphanet', 'MedGen:OMIM:Orphanet', 'MedGen:OMIM:Orphanet']	['C1836916:609033:ORPHA88628', 'C1836916:609033:ORPHA88628', 'C1836916:609033:ORPHA88628', 'C1836916:609033:ORPHA88628']	['Posterior_column_ataxia_with_retinitis_pigmentosa', 'Posterior_column_ataxia_with_retinitis_pigmentosa', 'Posterior_column_ataxia_with_retinitis_pigmentosa', 'Posterior_column_ataxia_with_retinitis_pigmentosa']	['single', 'single', 'conf', 'single']	['RCV000355025.1', 'RCV000297866.1', 'RCV000262602.1', 'RCV000351203.1']
1	215671030	C	T	NA12878_ERR194147	['NC_000001.11:g.215671031C>T']	[1]	['UniProtKB_(protein)']	[1]	['O75445#VAR_061351']	['255']	['MedGen']	['CN169374']	['not_specified']	['conf']	['RCV000041750.4']
1	237589773	AT	A	NA12878_ERR194147	['NC_000001.11:g.237589784delT']	[1]	['.']	[1]	['.']	['2\|255']	['MedGen:Orphanet:SNOMED_CT\|MedGen']	['C0878544:ORPHA167848:85898001\|CN169374']	['Cardiomyopathy\|not_specified']	['no_criteria\|conf']	['RCV000030420.1\|RCV000036734.8']
10	26088401	C	T	NA12878_ERR194147	['NC_000010.11:g.26088402C>T']	[1]	['.']	[1]	['.']	['255\|0']	['MedGen\|MedGen']	['CN169374\|CN239439']	['not_specified\|Nonsyndromic_Hearing_Loss\\x2c_Recessive']	['conf\|single']	['RCV000039026.3\|RCV000381484.1']
11	6392135	C	T	NA12878_ERR194147	['NC_000011.10:g.6392136C>T']	[1]	['.']	[1]	['.']	['255\|0']	['MedGen\|MedGen:SNOMED_CT']	['CN169374\|C0028064:58459009']	['not_specified\|Sphingomyelin/cholesterol_lipidosis']	['conf\|single']	['RCV000079188.5\|RCV000394529.1']
11	6617153	C	T	NA12878_ERR194147	['NC_000011.10:g.6617154C>A', 'NC_000011.10:g.6617154C>G', 'NC_000011.10:g.6617154C>T']	[1, 2, 3]	['.', 'OMIM_Allelic_Variant', '.']	[1, 1, 1]	['.', '607998.0004', '.']	['5', '5\|5\|5\|5\|5', '5']	['MedGen', 'MedGen:OMIM:Orphanet\|MedGen:OMIM:Orphanet\|MedGen\|MeSH:MedGen\|MedGen:OMIM:Orphanet:SNOMED_CT', 'MedGen']	['CN221809', 'C1876161:204500:ORPHA228349\|C1836474:609270:ORPHA284324\|CN221809\|D030342:C0950123\|C0027877:214200:ORPHA216:42012007', 'CN221809']	['not_provided', 'Ceroid_lipofuscinosis_neuronal_2\|Childhood-onset_autosomal_recessive_slowly_progressive_spinocerebellar_ataxia\|not_provided\|Inborn_genetic_diseases\|Neuronal_ceroid_lipofuscinosis', 'not_provided']	['single', 'mult\|single\|mult\|single\|single', 'single']	['RCV000391641.1', 'RCV000002763.11\|RCV000074608.7\|RCV000189765.4\|RCV000210689.1\|RCV000228119.2', 'RCV000189764.3']
11	47448802	C	T	NA12878_ERR194147	['NC_000011.10:g.47448803C>T']	[1]	['.']	[1]	['.']	['255']	['MedGen']	['CN169374']	['not_specified']	['conf']	['RCV000246056.2']
11	66510682	T	C	NA12878_ERR194147	['NC_000011.10:g.66510683T>C']	[1]	['.']	[1]	['.']	['255\|2']	['MedGen\|MedGen:OMIM:Orphanet:SNOMED_CT']	['CN169374\|C0752166:209900:ORPHA110:5619004']	['not_specified\|Bardet-Biedl_syndrome']	['conf\|single']	['RCV000173529.2\|RCV000226235.1']
12	102840473	T	C	NA12878_ERR194147	['NC_000012.12:g.102840474T>C']	[1]	['HGMD\|OMIM_Allelic_Variant\|UniProtKB_(protein)']	[1]	['CM910294\|612349.0017\|P00439#VAR_001038']	['5\|5\|5']	['MedGen\|MedGen\|MedGen:OMIM:Orphanet:SNOMED_CT']	['C0751435\|CN221809\|C0031485:261600:ORPHA716:154735006']	['Hyperphenylalaninemia\\x2c_non-pku\|not_provided\|Phenylketonuria']	['no_criteria\|single\|mult']	['RCV000000624.4\|RCV000078508.6\|RCV000150074.4']
14	23389061	AG	A	NA12878_ERR194147	['NC_000014.9:g.23389063delG']	[1]	['.']	[1]	['.']	['3\|255\|2\|0\|0\|0']	['MedGen:Orphanet:SNOMED_CT\|MedGen\|MedGen:OMIM\|MedGen:Orphanet\|MedGen\|Human_Phenotype_Ontology:MedGen:Orphanet']	['C0878544:ORPHA167848:85898001\|CN169374\|C2750467:613251\|C0018817:ORPHA1478\|CN239310\|HP:0001639:C0007194:ORPHA217569']	['Cardiomyopathy\|not_specified\|Familial_hypertrophic_cardiomyopathy_14\|Atrial_septal_defect\|Dilated_Cardiomyopathy\\x2c_Dominant\|Hypertrophic_cardiomyopathy']	['single\|conf\|single\|single\|single\|single']	['RCV000030306.1\|RCV000154759.3\|RCV000205051.2\|RCV000299696.1\|RCV000354591.1\|RCV000396023.1']
14	64210032	C	T	NA12878_ERR194147	['NC_000014.9:g.64210033C>T']	[2]	['OMIM_Allelic_Variant\|UniProtKB_(protein)']	[1]	['608442.0001\|Q8WXH0#VAR_062977']	['5\|255\|3']	['MedGen:OMIM\|MedGen\|MedGen:Orphanet:SNOMED_CT']	['C2751805:612999\|CN169374\|C0410189:ORPHA261:111508004']	['Emery-Dreifuss_muscular_dystrophy_5\\x2c_autosomal_dominant\|not_specified\|Emery-Dreifuss_muscular_dystrophy']	['no_criteria\|conf\|single']	['RCV000002414.4\|RCV000173937.3\|RCV000403391.1']
15	65078011	C	T	NA12878_ERR194147	['NC_000015.10:g.65078012C>T']	[1]	['.']	[1]	['.']	['255\|3']	['MedGen\|MedGen']	['CN169374\|CN239448']	['not_specified\|Nemaline_Myopathy\\x2c_Dominant']	['conf\|single']	['RCV000117307.4\|RCV000304321.1']
15	89645160	A	T	NA12878_ERR194147	['NC_000015.10:g.89645161A>T']	[1]	['.']	[1]	['.']	['255\|3']	['MedGen\|Gene:MedGen:OMIM:Orphanet']	['CN169374\|46:C0796147:200990:ORPHA36']	['not_specified\|Acrocallosal_syndrome\\x2c_Schinzel_type']	['conf\|single']	['RCV000117416.4\|RCV000261344.1']
16	2497032	C	G	NA12878_ERR194147	['NC_000016.10:g.2497033C>G']	[1]	['UniProtKB_(protein)']	[1]	['Q9ULP9#VAR_070890']	['255\|3\|3\|3']	['MedGen\|MedGen\|MedGen:OMIM\|MedGen:OMIM']	['CN169374\|C3809181\|C3892048:616044\|C3463992:308350']	['not_specified\|Caused_by_mutation_in_the_TBC1_domain_family\\x2c_member_24\|Deafness\\x2c_autosomal_dominant_65\|Epileptic_encephalopathy\\x2c_early_infantile\\x2c_1']	['conf\|single\|single\|single']	['RCV000128367.6\|RCV000477643.1\|RCV000477643.1\|RCV000477643.1']
16	56514588	C	T	NA12878_ERR194147	['NC_000016.10:g.56514589C\\x3d', 'NC_000016.10:g.56514589C>T']	[0, 1]	['OMIM_Allelic_Variant', '.']	[1, 1]	['606151.0013', '.']	['5', '2']	['MedGen', 'MedGen']	['C4016908', 'CN169374']	['Bardet-biedl_syndrome_2/6\\x2c_digenic', 'not_specified']	['no_criteria', 'single']	['RCV000004838.4', 'RCV000301991.1']
16	88805736	T	C	NA12878_ERR194147	['NC_000016.10:g.88805737T>C']	[1]	['UniProtKB_(protein)']	[1]	['Q9H211#VAR_054504']	['255']	['MedGen']	['CN169374']	['not_specified']	['conf']	['RCV000116652.3']
17	17796722	AAGG	A	NA12878_ERR194147	['NC_000017.11:g.17796729_17796731delGAG']	[1]	['HGMD']	[1]	['CD116392']	['255\|0']	['MedGen\|MedGen']	['CN169374\|CN221809']	['not_specified\|not_provided']	['conf\|single']	['RCV000082265.6\|RCV000118114.3']
18	2700878	A	G	NA12878_ERR194147	['NC_000018.10:g.2700879A>G']	[1]	['.']	[1]	['.']	['255']	['MedGen']	['CN169374']	['not_specified']	['conf']	['RCV000247697.2']
19	11132530	C	CA	NA12878_ERR194147	['NC_000019.10:g.11125285_11132532dup7248', 'NC_000019.10:g.11132532dupA']	[-1, 1]	['LDLR_@_LOVD', '.']	[5, 1]	['LDLR_000294', '.']	['255', '3']	['MedGen:OMIM:SNOMED_CT:SNOMED_CT', 'MedGen:OMIM:SNOMED_CT:SNOMED_CT']	['C0020445:143890:397915002:398036000', 'C0020445:143890:397915002:398036000']	['Familial_hypercholesterolemia', 'Familial_hypercholesterolemia']	['conf', 'single']	['RCV000237281.1', 'RCV000326993.1']
19	41414124	C	T	NA12878_ERR194147	['NC_000019.10:g.41414125C>T']	[1]	['HGMD\|UniProtKB_(protein)']	[1]	['CM021497\|P12694#VAR_034361']	['255\|3']	['MedGen\|MedGen:OMIM:Orphanet:SNOMED_CT']	['CN169374\|C0024776:248600:ORPHA268184:27718001']	['not_specified\|Maple_syrup_urine_disease']	['conf\|single']	['RCV000079243.6\|RCV000295914.1']
19	45179661	C	T	NA12878_ERR194147	['NC_000019.10:g.45179662C>T']	[1]	['.']	[1]	['.']	['255\|0']	['MedGen\|MedGen:SNOMED_CT']	['CN169374\|C0079504:9311003']	['not_specified\|Hermansky-Pudlak_syndrome']	['conf\|single']	['RCV000150192.3\|RCV000320201.1']
19	57231145	G	GC	NA12878_ERR194147	['NC_000019.10:g.57231150dupC']	[1]	['.']	[1]	['.']	['255']	['MedGen']	['CN239485']	['Spermatogenic_Failure']	['conf']	['RCV000311416.1']
2	178532038	C	T	NA12878_ERR194147	['NC_000002.12:g.178532039C>T']	[1]	['.']	[1]	['.']	['255\|2\|2\|2\|3\|3\|3\|3\|3\|3']	['MedGen\|MedGen:OMIM\|MedGen:OMIM:Orphanet\|MedGen\|MedGen:OMIM:Orphanet\|MedGen\|Human_Phenotype_Ontology:MedGen:Orphanet\|MedGen\|MedGen:OMIM:Orphanet\|MedGen:OMIM:Orphanet']	['CN169374\|C1858763:604145\|C1837342:608807:ORPHA140922\|CN230736\|C2673677:611705:ORPHA289377\|CN239352\|HP:0001639:C0007194:ORPHA217569\|CN239310\|C1863599:603689:ORPHA178464\|C1838244:600334:ORPHA609']	['not_specified\|Dilated_cardiomyopathy_1G\|Limb-girdle_muscular_dystrophy\\x2c_type_2J\|Cardiovascular_phenotype\|Myopathy\\x2c_early-onset\\x2c_with_fatal_cardiomyopathy\|Limb-Girdle_Muscular_Dystrophy\\x2c_Recessive\|Hypertrophic_cardiomyopathy\|Dilated_Cardiomyopathy\\x2c_Dominant\|Hereditary_myopathy_with_early_respiratory_failure\|Distal_myopathy_Markesbery-Griggs_type']	['conf\|single\|single\|single\|single\|single\|single\|single\|single\|single']	['RCV000040944.8\|RCV000231098.2\|RCV000231098.2\|RCV000244925.1\|RCV000296735.1\|RCV000311858.1\|RCV000336579.1\|RCV000351463.1\|RCV000402951.1\|RCV000403378.1']

Interactive Variant Annotation