chr6:6174866:G>A Detail (hg19) (F13A1)

Information

Genome

Assembly Position
hg19 chr6:6,174,866-6,174,866
hg38 chr6:6,174,633-6,174,633 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000129.3:c.1694C>T NP_000120.2:p.Pro565Leu
Ensemble ENST00000264870.8:c.1694C>T ENST00000264870.8:p.Pro565Leu
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.280
ToMMo:0.290
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.320

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
Review star
Show details
Links
Type Database ID Link
Gene MIM 134570 OMIM
HGNC 3531 HGNC
Ensembl ENSG00000124491 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv24153401 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
Benign 2021-08-10 criteria provided, multiple submitters, no conflicts Factor XIII, A subunit, deficiency of germline Detail
Conflicting interpretations of pathogenicity 2021-06-09 criteria provided, conflicting interpretations not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.155 myocardial infarction We therefore performed genotyping for factor XIIIA Val34Leu, Tyr204Phe and Pro56... BeFree 11841441 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000129.4(F13A1):c.1694C>T (p.Pro565Leu) AND not specified ClinVar Detail
NM_000129.4(F13A1):c.1694C>T (p.Pro565Leu) AND Factor XIII, A subunit, deficiency of ClinVar Detail
NM_000129.4(F13A1):c.1694C>T (p.Pro565Leu) AND not provided ClinVar Detail
We therefore performed genotyping for factor XIIIA Val34Leu, Tyr204Phe and Pro564Leu in a population... 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
rs5982 dbSNP
Genome
hg19
Position
chr6:6,174,866-6,174,866
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1182
Mean of sample read depth (HGVD)
78.47
Standard deviation of sample read depth (HGVD)
35.87
Number of reference allele (HGVD)
1701
Number of alternative allele (HGVD)
663
Allele Frequency (HGVD)
0.28045685279187815
Gene Symbol (HGVD)
F13A1
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))
rs5982
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.29
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4860
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8642
East Asian Allele Counts (ExAC)
2765
East Asian Heterozygous Counts (ExAC)
1921
East Asian Homozygous Counts (ExAC)
422
East Asian Allele Frequency (ExAC)
0.3199490858597547
Chromosome Counts in All Race (ExAC)
121394
Allele Counts in All Race (ExAC)
26216
Heterozygous Counts in All Race (ExAC)
19840
Homozygous Counts in All Race (ExAC)
3188
Allele Frequency in All Race (ExAC)
0.21595795508838986
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