Variant Detail

Variant Information
ID
DPV: 694
Chromosome
4
Gene
HGVS (GRCh37/hg19)
NC_000004.11:g.6302757T>C
HGVS (GRCh38/hg38)
NC_000004.12:g.6301030T>C
HGVS (RNA)
NM_001145853.1:c.1235T>C
HGVS (Protein)
NP_001139325.1:p.V412A
dbSNP
-
ClinGen Allele Registry
CA322524
Allele Frequency
Individual Information

ID
DPVS:160.1
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

Phenotype
-
Zygosity
unknown
Allele Origin
germline
Affected Status
no
Sample Type
  • DNA
Analysis Type
  • Next-Generation Sequencing - Illumina/Solexa
Collection Method
research
Compound heterozygous variant(s)
Data Submitter
Comment
-

ID
DPVS:3905.1
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
  • DNA
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.

ClinVar
Model Animals
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
4	6302757	NC_000004.11:g.6302757T>C	T	C	.	.	EXAC_AF=0.0008566;EXAC_AC=104;EXAC_AN=121412;GNOMAD_AF=0.00069986;GNOMAD_AC=176;GNOMAD_AN=251480;TOMMO_4_7K_AF=0.0092;TOMMO_4_7K_AC=88;TOMMO_4_7K_AN=9544;CLNALLELEID=211049;CLNDN=Wolfram_syndrome_1|Autosomal_dominant_nonsyndromic_deafness_6|not_specified|WFS1-Related_Spectrum_Disorders|not_provided;CLNDISDB=MONDO:MONDO:0009101,MedGen:C4551693,OMIM:222300|MONDO:MONDO:0010963,MedGen:C1833021,OMIM:600965|MedGen:CN169374|MedGen:CN239410|MedGen:CN517202;CLNSIG=Conflicting_interpretations_of_pathogenicity;CLNHGVS=NC_000004.11:g.6302757T>C;HGVD_AAF=0.007438;HGVD_NR=2402;HGVD_AC=18;GENEINFO=12762:7466;DPVID=694;DPVSIG=Benign|Pathogenic;DPVDSDBID=MedGen:C0018772;DPVDBN=Partial_deafness;DPVHGVS=NC_000004.11:g.6302757T>C	.
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-gr5qd3e4>
##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
4	6301030	NC_000004.11:g.6302757T>C	T	C	.	.	dbSNP_RSID=rs144951440;GNOMAD_AF=0.00069986;GNOMAD_AC=176;GNOMAD_AN=251480;CLNALLELEID=211049;CLNDN=Diabetes_mellitus_AND_insipidus_with_optic_atrophy_AND_deafness|Autosomal_dominant_nonsyndromic_deafness_6|not_specified|WFS1-Related_Spectrum_Disorders|not_provided;CLNDISDB=MONDO:MONDO:0009101,MedGen:C4551693,OMIM:222300,Orphanet:ORPHA3463,SNOMED_CT:70694009|MONDO:MONDO:0010963,MedGen:C1833021,OMIM:600965|MedGen:CN169374|MedGen:CN239410|MedGen:CN517202;CLNSIG=Conflicting_interpretations_of_pathogenicity;CLNHGVS=NC_000004.12:g.6301030T>C;GENEINFO=12762:7466;DPVID=694;DPVSIG=Benign|Pathogenic;DPVDSDBID=MedGen:C0018772;DPVDBN=Partial_deafness;DPVHGVS=NC_000004.12:g.6301030T>C	.