chr1:169519049:T>C Detail (hg19) (F5)

Information

Genome

Assembly Position
hg19 chr1:169,519,049-169,519,049
hg38 chr1:169,549,811-169,549,811 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000130.4:c.1601A>G NP_000121.2:p.Gln534Arg
Ensemble ENST00000367797.9:c.1601A>G ENST00000367797.9:p.Gln534Arg
ENST00000367796.3:c.1601A>G ENST00000367796.3:p.Gln534Arg
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:1.000
ToMMo:1.000
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:1.000

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 tgv3710551 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Conflicting interpretations of pathogenicity 2022-02-01 criteria provided, conflicting interpretations not provided germline unknown Detail
Benign 2024-02-01 criteria provided, single submitter Congenital factor V deficiency germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_000130.5(F5):c.1601= (p.Arg534=) AND not provided ClinVar Detail
NM_000130.5(F5):c.1601= (p.Arg534=) AND Congenital factor V deficiency ClinVar 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
rs6025 dbSNP
Genome
hg19
Position
chr1:169,519,049-169,519,049
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1180
Mean of sample read depth (HGVD)
24.21
Standard deviation of sample read depth (HGVD)
12.05
Number of reference allele (HGVD)
0
Number of alternative allele (HGVD)
2355
Allele Frequency (HGVD)
1.0
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))
rs6025
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8618
East Asian Allele Counts (ExAC)
8618
East Asian Heterozygous Counts (ExAC)
0
East Asian Homozygous Counts (ExAC)
4309
East Asian Allele Frequency (ExAC)
1.0
Chromosome Counts in All Race (ExAC)
121322
Allele Counts in All Race (ExAC)
118714
Heterozygous Counts in All Race (ExAC)
2520
Homozygous Counts in All Race (ExAC)
58097
Allele Frequency in All Race (ExAC)
0.9785034865894067
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