Variant Detail

Variant Information
ID
DPV: 638
Chromosome
21
Gene
HGVS (GRCh37/hg19)
NC_000021.8:g.27327998C>G
HGVS (GRCh38/hg38)
NC_000021.9:g.25955684C>G
HGVS (RNA)
NM_000484.3:c.1530G>C
HGVS (Protein)
NP_000475.1:p.K510N
dbSNP
-
ClinGen Allele Registry
CA9987289
Allele Frequency
Individual Information

ID
DPVS:426.1
Clinical Significance
Likely pathogenic
Date Last Evaluated
2015-06-11
Clinical Significance Citation
Yagi, R. Detecting gene mutations in Japanese Alzheimer's patients by semiconductor sequencing. 2014 Neurobiol Aging. 2014 Jul;35(7):1780.e1-5. doi: 10.1016/j.neurobiolaging.2014.01.023. Epub 2014 Jan 25. PMID:24559647

ICSID:2010127819

Transcript
-
Disease

Alzheimer disease 1, familial

Phenotype
-
Zygosity
single heterozygote
Allele Origin
inherited
Affected Status
unknown
Sample Type
  • DNA
Analysis Type
  • SEQuencing
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
Kensaku Kasuga, Masataka Kikuchi, Takayoshi Tokutake, Akihiro Nakaya, Toshiyuki Tezuka, Tamao Tsukie, Norikazu Hara, Akinori Miyashita, Ryozo Kuwano and Takeshi Ikeuchi. Systematic review and meta-analysis of Japanese familial Alzheimer's disease and FTDP-17. Journal of Human Genetics (2015) 60, 281-283; doi:10.1038/jhg.2015.15

ID
DPVS:5434.1
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
21	27327998	NC_000021.8:g.27327998C>G	C	G	.	.	EXAC_AF=8.236e-06;EXAC_AC=1;EXAC_AN=121412;GNOMAD_AF=3.9766e-06;GNOMAD_AC=1;GNOMAD_AN=251472;TOMMO_4_7K_AF=0.0024;TOMMO_4_7K_AC=23;TOMMO_4_7K_AN=9546;CLNALLELEID=886658;CLNDN=Alzheimer_disease;CLNDISDB=Human_Phenotype_Ontology:HP:0002511,Human_Phenotype_Ontology:HP:0006878,Human_Phenotype_Ontology:HP:0007213,MONDO:MONDO:0004975,MedGen:C0002395,OMIM:104300,SNOMED_CT:26929004;CLNSIG=Uncertain_significance;CLNHGVS=NC_000021.8:g.27327998C>G;HGVD_AAF=0.004296;HGVD_NR=2318;HGVD_AC=10;GENEINFO=620:351;DPVID=638;DPVSIG=Benign|Likely_pathogenic;DPVDSDBID=OMIM:104300;DPVDBN=Alzheimer_disease_1;DPVHGVS=NC_000021.8:g.27327998C>G	.
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-8d08r8uk>
##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
21	25955684	NC_000021.8:g.27327998C>G	C	G	.	.	dbSNP_RSID=rs767201930;GNOMAD_AF=3.9766e-06;GNOMAD_AC=1;GNOMAD_AN=251472;CLNALLELEID=886658;CLNDN=Alzheimer_disease;CLNDISDB=Human_Phenotype_Ontology:HP:0002511,Human_Phenotype_Ontology:HP:0006878,Human_Phenotype_Ontology:HP:0007213,MONDO:MONDO:0004975,MedGen:C0002395,OMIM:104300,SNOMED_CT:26929004;CLNSIG=Uncertain_significance;CLNHGVS=NC_000021.9:g.25955684C>G;GENEINFO=620:351;DPVID=638;DPVSIG=Benign|Likely_pathogenic;DPVDSDBID=OMIM:104300;DPVDBN=Alzheimer_disease_1;DPVHGVS=NC_000021.9:g.25955684C>G	.