chr10:124221276:G>T Detail (hg19) (HTRA1, ARMS2)

Information

Genome

Assembly Position
hg19 chr10:124,221,276-124,221,276
hg38 chr10:122,461,760-122,461,760 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_002775.4:c.108G>T NP_002766.1:p.Gly36=
Ensemble ENST00000648167.1:c.154+3051G>T
ENST00000368984.8:c.108G>T ENST00000368984.8:p.Gly36=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.373
ToMMo:0.357
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.429

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 602194 OMIM
HGNC 9476 HGNC
Ensembl ENSG00000166033 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv40934649 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2017-06-01 criteria provided, single submitter CARASIL syndrome germline unknown Detail
Likely benign 2016-06-14 criteria provided, single submitter macular degeneration germline Detail
Benign 2024-01-29 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.005 macular degeneration The coding HTRA1 SNP rs2293870, not part of the significant haplotypes containin... BeFree 18164066 Detail
0.267 age related macular degeneration The coding HTRA1 SNP rs2293870, not part of the significant haplotypes containin... BeFree 18164066 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002775.5(HTRA1):c.108G>T (p.Gly36=) AND CARASIL syndrome ClinVar Detail
NM_002775.5(HTRA1):c.108G>T (p.Gly36=) AND Macular degeneration ClinVar Detail
NM_002775.5(HTRA1):c.108G>T (p.Gly36=) AND not provided ClinVar Detail
The coding HTRA1 SNP rs2293870, not part of the significant haplotypes containing rs10490924 and rs1... DisGeNET Detail
The coding HTRA1 SNP rs2293870, not part of the significant haplotypes containing rs10490924 and rs1... 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
rs2293870 dbSNP
Genome
hg19
Position
chr10:124,221,276-124,221,276
Variant Type
snv
Reference Allele
G
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
806
Mean of sample read depth (HGVD)
15.77
Standard deviation of sample read depth (HGVD)
7.59
Number of reference allele (HGVD)
1011
Number of alternative allele (HGVD)
601
Allele Frequency (HGVD)
0.3728287841191067
Gene Symbol (HGVD)
HTRA1
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))
rs2293870
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3568
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5968
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16728
East Asian Chromosome Counts (ExAC)
42
East Asian Allele Counts (ExAC)
18
East Asian Heterozygous Counts (ExAC)
10
East Asian Homozygous Counts (ExAC)
4
East Asian Allele Frequency (ExAC)
0.42857142857142855
Chromosome Counts in All Race (ExAC)
2310
Allele Counts in All Race (ExAC)
948
Heterozygous Counts in All Race (ExAC)
548
Homozygous Counts in All Race (ExAC)
188
Allele Frequency in All Race (ExAC)
0.4103896103896104
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