chr1:109272630:A>G Detail (hg38) (CELSR2)

Information

Genome

Assembly Position
hg19 chr1:109,815,252-109,815,252 View the variant detail on this assembly version.
hg38 chr1:109,272,630-109,272,630

HGVS

Type Transcript Protein
RefSeq NM_001408.2:c.8055-10A>G
Ensemble ENST00000271332.4:c.8055-10A>G
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.087
ToMMo:0.070
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.066

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 604265 OMIM
HGNC 3231 HGNC
Ensembl ENSG00000143126 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv2747808 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-29 criteria provided, single submitter not provided germline Detail
Benign 2019-10-21 criteria provided, single submitter CELSR2-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.126 coronary artery disease CAD association was replicated and/or verified for 4 loci: SORT1 rs611917 (p=1.7... BeFree 23050023 Detail
0.125 coronary artery disease CAD association was replicated and/or verified for 4 loci: SORT1 rs611917 (p=1.7... BeFree 23050023 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001408.3(CELSR2):c.8055-10A>G AND not provided ClinVar Detail
NM_001408.3(CELSR2):c.8055-10A>G AND CELSR2-related disorder ClinVar Detail
CAD association was replicated and/or verified for 4 loci: SORT1 rs611917 (p=1.7 × 10(-8)), APOA5 rs... DisGeNET Detail
CAD association was replicated and/or verified for 4 loci: SORT1 rs611917 (p=1.7 × 10(-8)), APOA5 rs... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs611917 dbSNP
Genome
hg38
Position
chr1:109,272,630-109,272,630
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1203
Mean of sample read depth (HGVD)
59.35
Standard deviation of sample read depth (HGVD)
28.67
Number of reference allele (HGVD)
2197
Number of alternative allele (HGVD)
209
Allele Frequency (HGVD)
0.08686616791354947
Gene Symbol (HGVD)
CELSR2
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))
rs611917
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0699
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1171
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8536
East Asian Allele Counts (ExAC)
563
East Asian Heterozygous Counts (ExAC)
529
East Asian Homozygous Counts (ExAC)
17
East Asian Allele Frequency (ExAC)
0.06595595126522961
Chromosome Counts in All Race (ExAC)
117754
Allele Counts in All Race (ExAC)
33740
Heterozygous Counts in All Race (ExAC)
23556
Homozygous Counts in All Race (ExAC)
5092
Allele Frequency in All Race (ExAC)
0.28652954464391867
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