chr13:110818598:T>G Detail (hg19) (COL4A1)

Information

Genome

Assembly Position
hg19 chr13:110,818,598-110,818,598
hg38 chr13:110,166,251-110,166,251 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001845.5:c.4002A>C NP_001836.3:p.Gln1334His
Ensemble ENST00000375820.10:c.4002A>C ENST00000375820.10:p.Gln1334His
ENST00000615732.3:c.3810A>C ENST00000615732.3:p.Gln1270His
Summary

MGeND

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

Frequency

JP HGVD:0.258
ToMMo:0.264
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.250

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 120130 OMIM
HGNC 2202 HGNC
Ensembl ENSG00000187498 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv49865679 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 2018-01-15 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2016-06-14 criteria provided, single submitter Porencephalic cyst germline Detail
Benign 2021-07-22 criteria provided, multiple submitters, no conflicts Autosomal dominant familial hematuria-retinal arteriolar tortuosity-contractures syndrome germline Detail
Benign 2024-02-01 criteria provided, single submitter not provided germline Detail
Benign 2021-07-22 criteria provided, multiple submitters, no conflicts Brain small vessel disease 1 with or without ocular anomalies germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Hypercholesterolemia Further examination by multivariable logistic regression analysis with adjustmen... BeFree 18077766 Detail
0.002 Mental disorders [A genome-wide association study identified a SNP in the COL4A1 gene that was si... GAD 20031579 Detail
<0.001 Hypercholesterolemia Further examination by multivariable logistic regression analysis with adjustmen... BeFree 18077766 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001845.6(COL4A1):c.4002A>C (p.Gln1334His) AND not specified ClinVar Detail
NM_001845.6(COL4A1):c.4002A>C (p.Gln1334His) AND Porencephalic cyst ClinVar Detail
NM_001845.6(COL4A1):c.4002A>C (p.Gln1334His) AND Autosomal dominant familial hematuria-retinal arter... ClinVar Detail
NM_001845.6(COL4A1):c.4002A>C (p.Gln1334His) AND not provided ClinVar Detail
NM_001845.6(COL4A1):c.4002A>C (p.Gln1334His) AND Brain small vessel disease 1 with or without ocular... ClinVar Detail
Further examination by multivariable logistic regression analysis with adjustment for age, sex, body... DisGeNET Detail
[A genome-wide association study identified a SNP in the COL4A1 gene that was significantly associat... DisGeNET Detail
Further examination by multivariable logistic regression analysis with adjustment for age, sex, body... 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
rs3742207 dbSNP
Genome
hg19
Position
chr13:110,818,598-110,818,598
Variant Type
snv
Reference Allele
T
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1189
Mean of sample read depth (HGVD)
49.51
Standard deviation of sample read depth (HGVD)
26.61
Number of reference allele (HGVD)
1765
Number of alternative allele (HGVD)
613
Allele Frequency (HGVD)
0.25777964676198484
Gene Symbol (HGVD)
COL4A1
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))
rs3742207
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2643
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4430
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8648
East Asian Allele Counts (ExAC)
2162
East Asian Heterozygous Counts (ExAC)
1648
East Asian Homozygous Counts (ExAC)
257
East Asian Allele Frequency (ExAC)
0.25
Chromosome Counts in All Race (ExAC)
121398
Allele Counts in All Race (ExAC)
37608
Heterozygous Counts in All Race (ExAC)
25535
Homozygous Counts in All Race (ExAC)
6036
Allele Frequency in All Race (ExAC)
0.309790935600257
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