chr6:31936027:G>C Detail (hg38) (C2, C2-AS1)

Information

Genome

Assembly Position
hg19 chr6:31,903,804-31,903,804 View the variant detail on this assembly version.
hg38 chr6:31,936,027-31,936,027

HGVS

Type Transcript Protein
RefSeq NM_000063.5:c.954G>C NP_000054.2:p.Glu318Asp
NM_001282458.1:c.954G>C NP_001269387.1:p.Glu318Asp
NM_001145903.2:c.558G>C NP_001139375.1:p.Glu186Asp
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.021
ToMMo:0.030
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.017

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 613927 OMIM
HGNC 1248 HGNC
Ensembl ENSG00000166278 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv24803835 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Likely benign 2017-04-27 criteria provided, single submitter age related macular degeneration 14 germline Detail
Benign Likely benign 2019-05-28 criteria provided, multiple submitters, no conflicts complement component 2 deficiency germline unknown Detail
Benign 2016-03-28 criteria provided, single submitter not specified germline Detail
Benign 2024-01-29 criteria provided, multiple submitters, no conflicts not provided germline Detail
Likely benign 2022-04-09 criteria provided, single submitter complement component 2 deficiency,age related macular degeneration 14 unknown Detail
Likely benign 2022-04-09 criteria provided, single submitter complement component 2 deficiency,age related macular degeneration 14 unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.292 age related macular degeneration No association with AMD was found for SNP rs9332739 (E318D) in the C2 gene or fo... BeFree 18806293 Detail
0.319 age related macular degeneration We performed an association analysis between PCV and polymorphisms across the C2... BeFree 19556007 Detail
0.292 age related macular degeneration Heritability and genome-wide association study to assess genetic differences bet... GWASCAT 22705344 Detail
0.292 age related macular degeneration Common variants near FRK/COL10A1 and VEGFA are associated with advanced age-rela... GWASCAT 21665990 Detail
0.120 age related macular degeneration Common variants near FRK/COL10A1 and VEGFA are associated with advanced age-rela... GWASCAT 21665990 Detail
0.120 age related macular degeneration Heritability and genome-wide association study to assess genetic differences bet... GWASCAT 22705344 Detail
0.292 age related macular degeneration [The significant association is retained following multivariate analysis with ad... GAD 20157618 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000063.6(C2):c.954G>C (p.Glu318Asp) AND Age related macular degeneration 14 ClinVar Detail
NM_000063.6(C2):c.954G>C (p.Glu318Asp) AND Complement component 2 deficiency ClinVar Detail
NM_000063.6(C2):c.954G>C (p.Glu318Asp) AND not specified ClinVar Detail
NM_000063.6(C2):c.954G>C (p.Glu318Asp) AND not provided ClinVar Detail
NM_000063.6(C2):c.954G>C (p.Glu318Asp) AND multiple conditions ClinVar Detail
NM_000063.6(C2):c.954G>C (p.Glu318Asp) AND multiple conditions ClinVar Detail
No association with AMD was found for SNP rs9332739 (E318D) in the C2 gene or for rs4151667 (L9H), r... DisGeNET Detail
We performed an association analysis between PCV and polymorphisms across the C2-CFB-RDBP-SKIV2L reg... DisGeNET Detail
Heritability and genome-wide association study to assess genetic differences between advanced age-re... DisGeNET Detail
Common variants near FRK/COL10A1 and VEGFA are associated with advanced age-related macular degenera... DisGeNET Detail
Common variants near FRK/COL10A1 and VEGFA are associated with advanced age-related macular degenera... DisGeNET Detail
Heritability and genome-wide association study to assess genetic differences between advanced age-re... DisGeNET Detail
[The significant association is retained following multivariate analysis with adjustment for age, sm... 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
rs9332739 dbSNP
Genome
hg38
Position
chr6:31,936,027-31,936,027
Variant Type
snv
Reference Allele
G
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1172
Mean of sample read depth (HGVD)
115.90
Standard deviation of sample read depth (HGVD)
56.54
Number of reference allele (HGVD)
2295
Number of alternative allele (HGVD)
49
Allele Frequency (HGVD)
0.020904436860068258
Gene Symbol (HGVD)
C2
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))
rs9332739
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0298
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
500
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8506
East Asian Allele Counts (ExAC)
147
East Asian Heterozygous Counts (ExAC)
141
East Asian Homozygous Counts (ExAC)
3
East Asian Allele Frequency (ExAC)
0.017281918645661885
Chromosome Counts in All Race (ExAC)
116040
Allele Counts in All Race (ExAC)
4521
Heterozygous Counts in All Race (ExAC)
4317
Homozygous Counts in All Race (ExAC)
102
Allele Frequency in All Race (ExAC)
0.038960703205791106
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