chr2:189943266:C>G Detail (hg19) (COL5A2)

Information

Genome

Assembly Position
hg19 chr2:189,943,266-189,943,266
hg38 chr2:189,078,540-189,078,540 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000393.3:c.1035G>C NP_000384.2:p.Gly345=
Ensemble ENST00000374866.9:c.1035G>C ENST00000374866.9:p.Gly345=
ENST00000618828.1:c.358+540G>C
Summary

MGeND

Clinical significance Benign
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.013
ToMMo:0.009
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.021

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 120190 OMIM
HGNC 2210 HGNC
Ensembl ENSG00000204262 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv9887645 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign Centenarian germline MGS000068
(TMGS000140) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2013-09-11 criteria provided, single submitter not specified germline Detail
Likely benign 2016-06-14 criteria provided, single submitter Ehlers-Danlos syndrome type 7A germline Detail
Benign 2024-01-29 criteria provided, single submitter Ehlers-Danlos syndrome, classic type, 1 germline Detail
Benign 2018-07-10 criteria provided, multiple submitters, no conflicts Ehlers-Danlos syndrome, classic type, 2 germline Detail
Benign 2015-09-27 criteria provided, single submitter Familial thoracic aortic aneurysm and aortic dissection germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_000393.5(COL5A2):c.1035G>C (p.Gly345=) AND not specified ClinVar Detail
NM_000393.5(COL5A2):c.1035G>C (p.Gly345=) AND Ehlers-Danlos syndrome type 7A ClinVar Detail
NM_000393.5(COL5A2):c.1035G>C (p.Gly345=) AND Ehlers-Danlos syndrome, classic type, 1 ClinVar Detail
NM_000393.5(COL5A2):c.1035G>C (p.Gly345=) AND Ehlers-Danlos syndrome, classic type, 2 ClinVar Detail
NM_000393.5(COL5A2):c.1035G>C (p.Gly345=) AND Familial thoracic aortic aneurysm and aortic dissectio... 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
rs148786600 dbSNP
Genome
hg19
Position
chr2:189,943,266-189,943,266
Variant Type
snv
Reference Allele
C
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1157
Mean of sample read depth (HGVD)
34.64
Standard deviation of sample read depth (HGVD)
44.28
Number of reference allele (HGVD)
2284
Number of alternative allele (HGVD)
30
Allele Frequency (HGVD)
0.01296456352636128
Gene Symbol (HGVD)
COL5A2
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))
rs148786600
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0089
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
150
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8654
East Asian Allele Counts (ExAC)
184
East Asian Heterozygous Counts (ExAC)
182
East Asian Homozygous Counts (ExAC)
1
East Asian Allele Frequency (ExAC)
0.021261844233880285
Chromosome Counts in All Race (ExAC)
121398
Allele Counts in All Race (ExAC)
198
Heterozygous Counts in All Race (ExAC)
196
Homozygous Counts in All Race (ExAC)
1
Allele Frequency in All Race (ExAC)
0.0016309988632432165
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