chr15:51507968:G>A Detail (hg19) (CYP19A1, PIRC66, MIR4713HG)

Information

Genome

Assembly Position
hg19 chr15:51,507,968-51,507,968
hg38 chr15:51,215,771-51,215,771 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_031226.2:c.790C>T NP_112503.1:p.Arg264Cys
NM_000103.3:c.790C>T NP_000094.2:p.Arg264Cys
Ensemble ENST00000396404.8:c.790C>T ENST00000396404.8:p.Arg264Cys
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.258
ToMMo:0.281
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.138

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 107910 OMIM
HGNC 2594 HGNC
Ensembl ENSG00000137869 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv52937008 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2014-05-12 criteria provided, single submitter not specified germline Detail
Benign 2018-03-06 criteria provided, single submitter Aromatase deficiency germline Detail
Benign 2024-02-01 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.017 breast carcinoma We examined the association of single nucleotide polymorphism (SNP) in estrogen ... BeFree 24430361 Detail
0.097 Malignant neoplasm of breast We examined the association of single nucleotide polymorphism (SNP) in estrogen ... BeFree 24430361 Detail
0.068 Malignant neoplasm of breast We examined the association of single nucleotide polymorphism (SNP) in estrogen ... BeFree 24430361 Detail
0.030 breast carcinoma We examined the association of single nucleotide polymorphism (SNP) in estrogen ... BeFree 24430361 Detail
0.240 endometriosis Here, we evaluated whether the risk and severity of endometriosis are associated... BeFree 15640252 Detail
0.006 Mammographic Density [The CYP19A1 rs936306 TT genotype was associated with 6.2% lower mammographic de... GAD 19630952 Detail
0.123 Ovarian Diseases The Arg(264)Cys variant of CYP19A1 (rs700519) is associated with PCOS (P= 0.004,... BeFree 21282199 Detail
0.114 Malignant neoplasm of breast The results suggest that the CYP19 Arg(264)Cys polymorphism modifies breast canc... BeFree 12618873 Detail
0.033 breast carcinoma The results suggest that the CYP19 Arg(264)Cys polymorphism modifies breast canc... BeFree 12618873 Detail
0.017 breast carcinoma The results suggest that the CYP19 Arg(264)Cys polymorphism modifies breast canc... BeFree 12618873 Detail
0.097 Malignant neoplasm of breast The results suggest that the CYP19 Arg(264)Cys polymorphism modifies breast canc... BeFree 12618873 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000103.4(CYP19A1):c.790C>T (p.Arg264Cys) AND not specified ClinVar Detail
NM_000103.4(CYP19A1):c.790C>T (p.Arg264Cys) AND Aromatase deficiency ClinVar Detail
NM_000103.4(CYP19A1):c.790C>T (p.Arg264Cys) AND not provided ClinVar Detail
We examined the association of single nucleotide polymorphism (SNP) in estrogen receptors, ESR1 (rs2... DisGeNET Detail
We examined the association of single nucleotide polymorphism (SNP) in estrogen receptors, ESR1 (rs2... DisGeNET Detail
We examined the association of single nucleotide polymorphism (SNP) in estrogen receptors, ESR1 (rs2... DisGeNET Detail
We examined the association of single nucleotide polymorphism (SNP) in estrogen receptors, ESR1 (rs2... DisGeNET Detail
Here, we evaluated whether the risk and severity of endometriosis are associated with polymorphisms ... DisGeNET Detail
[The CYP19A1 rs936306 TT genotype was associated with 6.2% lower mammographic density than the TC/CC... DisGeNET Detail
The Arg(264)Cys variant of CYP19A1 (rs700519) is associated with PCOS (P= 0.004, corrected P = 0.02)... DisGeNET Detail
The results suggest that the CYP19 Arg(264)Cys polymorphism modifies breast cancer risk (OR=1.5, 95%... DisGeNET Detail
The results suggest that the CYP19 Arg(264)Cys polymorphism modifies breast cancer risk (OR=1.5, 95%... DisGeNET Detail
The results suggest that the CYP19 Arg(264)Cys polymorphism modifies breast cancer risk (OR=1.5, 95%... DisGeNET Detail
The results suggest that the CYP19 Arg(264)Cys polymorphism modifies breast cancer risk (OR=1.5, 95%... 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
rs700519 dbSNP
Genome
hg19
Position
chr15:51,507,968-51,507,968
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
159.58
Standard deviation of sample read depth (HGVD)
72.32
Number of reference allele (HGVD)
1795
Number of alternative allele (HGVD)
625
Allele Frequency (HGVD)
0.25826446280991733
Gene Symbol (HGVD)
CYP19A1
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))
rs700519
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2814
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4716
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8636
East Asian Allele Counts (ExAC)
1195
East Asian Heterozygous Counts (ExAC)
1003
East Asian Homozygous Counts (ExAC)
96
East Asian Allele Frequency (ExAC)
0.13837424733672996
Chromosome Counts in All Race (ExAC)
121360
Allele Counts in All Race (ExAC)
9659
Heterozygous Counts in All Race (ExAC)
8127
Homozygous Counts in All Race (ExAC)
766
Allele Frequency in All Race (ExAC)
0.07958965062623599
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