chr1:169542517:T>C Detail (hg38) (F5)

Information

Genome

Assembly Position
hg19 chr1:169,511,755-169,511,755 View the variant detail on this assembly version.
hg38 chr1:169,542,517-169,542,517

HGVS

Type Transcript Protein
RefSeq NM_000130.4:c.2573A>G NP_000121.2:p.Lys858Arg
Ensemble ENST00000367796.3:c.2588A>G ENST00000367796.3:p.Lys863Arg
ENST00000367797.9:c.2573A>G ENST00000367797.9:p.Lys858Arg
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.214
ToMMo:0.232
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.219

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
Review star
Show details
Links
Type Database ID Link
Gene MIM 612309 OMIM
HGNC 3542 HGNC
Ensembl ENSG00000198734 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv3710179 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign criteria provided, single submitter not specified germline Detail
Likely benign 2017-04-27 criteria provided, single submitter thrombophilia due to activated protein C resistance germline Detail
Conflicting interpretations of pathogenicity 2018-11-11 criteria provided, conflicting interpretations not provided germline Detail
Benign 2024-02-01 criteria provided, single submitter Congenital factor V deficiency germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.355 Venous thromboembolism Meta-analysis of 65,734 individuals identifies TSPAN15 and SLC44A2 as two suscep... GWASCAT 25772935 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000130.5(F5):c.2573A>G (p.Lys858Arg) AND not specified ClinVar Detail
NM_000130.5(F5):c.2573A>G (p.Lys858Arg) AND Thrombophilia due to activated protein C resistance ClinVar Detail
NM_000130.5(F5):c.2573A>G (p.Lys858Arg) AND not provided ClinVar Detail
NM_000130.5(F5):c.2573A>G (p.Lys858Arg) AND Congenital factor V deficiency ClinVar Detail
Meta-analysis of 65,734 individuals identifies TSPAN15 and SLC44A2 as two susceptibility loci for ve... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs4524 dbSNP
Genome
hg38
Position
chr1:169,542,517-169,542,517
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1202
Mean of sample read depth (HGVD)
147.71
Standard deviation of sample read depth (HGVD)
64.21
Number of reference allele (HGVD)
1889
Number of alternative allele (HGVD)
514
Allele Frequency (HGVD)
0.21389929255097795
Gene Symbol (HGVD)
F5
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs4524
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.232
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3889
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8640
East Asian Allele Counts (ExAC)
1891
East Asian Heterozygous Counts (ExAC)
1471
East Asian Homozygous Counts (ExAC)
210
East Asian Allele Frequency (ExAC)
0.21886574074074075
Chromosome Counts in All Race (ExAC)
121332
Allele Counts in All Race (ExAC)
33590
Heterozygous Counts in All Race (ExAC)
23438
Homozygous Counts in All Race (ExAC)
5076
Allele Frequency in All Race (ExAC)
0.27684370157913823
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