Database of Pathogenic Variants

Individual Information

DPVS:197.1
DPVS:4159.1

ID

DPVS:197.1

Clinical Significance

Pathogenic

Date Last Evaluated

2017-03-30

Clinical Significance Citation

Moteki, H. Comprehensive genetic testing with ethnic-specific filtering by allele frequency in a Japanese hearing-loss population. 2016 Clin Genet. 2016 Apr;89(4):466-472. doi: 10.1111/cge.12677. Epub 2015 Oct 6. PMID:26346818

Transcript

Disease

Partial deafness
MedGen:C0018772

Phenotype

Zygosity

unknown

Allele Origin

germline

Affected Status

Sample Type

Analysis Type

Next-Generation Sequencing - Illumina/Solexa

Collection Method

research

Compound heterozygous variant(s)

Data Submitter

Comment

ID

DPVS:4159.1

Clinical Significance

Benign

Date Last Evaluated

2018-11-15

Clinical Significance Citation

Transcript

Disease

(Centenarian)

Phenotype

Zygosity

unknown

Allele Origin

germline

Affected Status

unknown

Sample Type

Analysis Type

Next-Generation Sequencing

Collection Method

research

Compound heterozygous variant(s)

Data Submitter

Comment

This variant was detected among a group of 300 centenarians by NGS and has not been confirmed by Sanger sequence. Considering that these individuals lives longer than 100 years, this variant could be considered "Benign" regardless of the allele frequency. However, no functional evaluation has been performed.

VCF

VCF (GRCh37/hg19)

											##fileformat=VCFv4.0
##reference=GRCh37
##INFO=<ID=CLNALLELEID,Number=1,Type=Integer,Description="the ClinVar Allele ID">
##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN (from ClinVar)">
##INFO=<ID=CLNDN,Number=.,Type=String,Description="ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB (from ClinVar)">
##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Top-level (primary assembly, alt, or patch) HGVS expression.(from ClinVar)">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Clinical significance for this single variant (from ClinVar)">
##INFO=<ID=EXAC_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from ExAC r1)">
##INFO=<ID=EXAC_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from ExAC r1)">
##INFO=<ID=EXAC_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from ExAC r1)">
##INFO=<ID=EXAC_FILTER,Number=1,Type=String,Description="calculated by self of overlapping values in field FILTER (from ExAC r1)">
##INFO=<ID=GNOMAD_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from gnomAD v2.1.1 )">
##INFO=<ID=HGVD_AAF,Number=A,Type=Float,Description="Alternative Allele Frequency(s) NA/(NR+NAtotal) (from HGVD/DBexome20170802)">
##INFO=<ID=HGVD_AC,Number=A,Type=Integer,Description="number(s) of alternative allele(s) (from HGVD/DBexome20170802)">
##INFO=<ID=HGVD_NR,Number=1,Type=Integer,Description="number of reference allele (from HGVD/DBexome20170802)">
##INFO=<ID=TOMMO_4_7K_AC,Number=A,Type=Integer,Description="Allele count in genotypes (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=TOMMO_4_7K_AF,Number=A,Type=Float,Description="Allele frequency, for each ALT allele, in the same order as listed  (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=TOMMO_4_7K_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=dbSNP_RSID,Number=1,Type=String,Description="dbSNP ID (from dbSNP b151 )">
##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:)">
##INFO=<ID=DPVID,Number=.,Type=String,Description="DPV Variant ID">
##INFO=<ID=DPVSIG,Number=.,Type=String,Description="Variant Clinical Significance">
##INFO=<ID=DPVDSDBID,Number=.,Type=String,Description="Variant disease database ID">
##INFO=<ID=DPVDBN,Number=.,Type=String,Description="Variant disease name">
##INFO=<ID=DPVHGVS,Number=.,Type=String,Description="Variant in HGVS.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
6	33154514	NC_000006.11:g.33154514C>A	C	A	.	.	EXAC_AF=0.0006424;EXAC_AC=78;EXAC_AN=121412;GNOMAD_AF=0.00077141;GNOMAD_AC=194;GNOMAD_AN=251488;TOMMO_4_7K_AF=0.0112;TOMMO_4_7K_AC=107;TOMMO_4_7K_AN=9546;CLNALLELEID=227296;CLNDN=Otospondylomegaepiphyseal_dysplasia,_autosomal_dominant|Deafness,_autosomal_dominant_13|Deafness,_autosomal_recessive_53|Fibrochondrogenesis_2|Otospondylomegaepiphyseal_dysplasia,_autosomal_recessive|not_specified|Stickler_Syndrome,_Dominant;CLNDISDB=MONDO:MONDO:0008490,MedGen:C1861481,OMIM:184840,Orphanet:ORPHA166100|MONDO:MONDO:0011159,MedGen:C1866095,OMIM:601868|MONDO:MONDO:0012333,MedGen:C1864746,OMIM:609706|MONDO:MONDO:0013795,MedGen:C3281128,OMIM:614524|MONDO:MONDO:0044206,MedGen:C4520892,OMIM:215150|MedGen:CN169374|MedGen:CN239460;CLNSIG=Conflicting_interpretations_of_pathogenicity;CLNHGVS=NC_000006.11:g.33154514C>A;HGVD_AAF=0.00906;HGVD_NR=2297;HGVD_AC=21;GENEINFO=2187:1302;DPVID=738;DPVSIG=Benign|Pathogenic;DPVDSDBID=MedGen:C0018772;DPVDBN=Partial_deafness;DPVHGVS=NC_000006.11:g.33154514C>A	.

VCF (GRCh38/hg38)

											##fileformat=VCFv4.0
##reference=GRCh38
##INFO=<ID=CLNALLELEID,Number=1,Type=Integer,Description="the ClinVar Allele ID">
##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN (from ClinVar)">
##INFO=<ID=CLNDN,Number=.,Type=String,Description="ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB (from ClinVar)">
##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Top-level (primary assembly, alt, or patch) HGVS expression.(from ClinVar)">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Clinical significance for this single variant (from ClinVar)">
##INFO=<ID=GNOMAD_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from gnomAD v2.1.1 )">
##INFO=<ID=dbSNP_RSID,Number=1,Type=String,Description="dbSNP ID (from dbSNP b151 )">
##originalFile=</tmp/crossmap-input-n7xr44sh>
##targetRefGenome=</usr/lib64/python2.7/site-packages/transvar/transvar.download/hg38.fa>
##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:)">
##INFO=<ID=DPVID,Number=.,Type=String,Description="DPV Variant ID">
##INFO=<ID=DPVSIG,Number=.,Type=String,Description="Variant Clinical Significance">
##INFO=<ID=DPVDSDBID,Number=.,Type=String,Description="Variant disease database ID">
##INFO=<ID=DPVDBN,Number=.,Type=String,Description="Variant disease name">
##INFO=<ID=DPVHGVS,Number=.,Type=String,Description="Variant in HGVS.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
6	33186737	NC_000006.11:g.33154514C>A	C	A	.	.	dbSNP_RSID=rs141430703;GNOMAD_AF=0.00077141;GNOMAD_AC=194;GNOMAD_AN=251488;CLNALLELEID=227296;CLNDN=Otospondylomegaepiphyseal_dysplasia,_autosomal_dominant|Deafness,_autosomal_dominant_13|Deafness,_autosomal_recessive_53|Fibrochondrogenesis_2|Otospondylomegaepiphyseal_dysplasia,_autosomal_recessive|not_specified|Stickler_Syndrome,_Dominant;CLNDISDB=MONDO:MONDO:0008490,MedGen:C1861481,OMIM:184840,Orphanet:ORPHA166100|MONDO:MONDO:0011159,MedGen:C1866095,OMIM:601868|MONDO:MONDO:0012333,MedGen:C1864746,OMIM:609706|MONDO:MONDO:0013795,MedGen:C3281128,OMIM:614524|MONDO:MONDO:0044206,MedGen:C4520892,OMIM:215150|MedGen:CN169374|MedGen:CN239460;CLNSIG=Conflicting_interpretations_of_pathogenicity;CLNHGVS=NC_000006.12:g.33186737C>A;GENEINFO=2187:1302;DPVID=738;DPVSIG=Benign|Pathogenic;DPVDSDBID=MedGen:C0018772;DPVDBN=Partial_deafness;DPVHGVS=NC_000006.12:g.33186737C>A	.

Variant Detail