chr9:97697296:T>C Detail (hg38) (XPA)

Information

Genome

Assembly Position
hg19 chr9:100,459,578-100,459,578 View the variant detail on this assembly version.
hg38 chr9:97,697,296-97,697,296

HGVS

Type Transcript Protein
RefSeq NM_000380.3:c.-4A>G
Ensemble ENST00000375128.5:c.-4A>G
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.503
ToMMo:0.505
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.498

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 611153 OMIM
HGNC 12814 HGNC
Ensembl ENSG00000136936 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv36960083 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-03-29 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2023-07-07 criteria provided, multiple submitters, no conflicts xeroderma pigmentosum group A germline Detail
Benign 2024-01-22 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.003 lymphoma Herein we performed a case-control study evaluating the influence of three singl... BeFree 23818366 Detail
0.003 lymphoma Herein we performed a case-control study evaluating the influence of three singl... BeFree 23818366 Detail
0.136 lymphoma Herein we performed a case-control study evaluating the influence of three singl... BeFree 23818366 Detail
0.018 breast carcinoma Our findings provide clear evidence that XRCC1 gene rs25487 and XPA gene rs18009... BeFree 24642895 Detail
0.084 Malignant neoplasm of breast Moreover, the T-G (including rs2808668 and rs1800975) haplotype in XPA combined ... BeFree 21751184 Detail
0.014 squamous cell carcinoma Although smoking is the dominant risk factor of lung cancer, XPA -4G>A (rs180... BeFree 21195504 Detail
0.098 Malignant neoplasm of breast Our findings provide clear evidence that XRCC1 gene rs25487 and XPA gene rs18009... BeFree 24642895 Detail
0.008 breast carcinoma Moreover, the T-G (including rs2808668 and rs1800975) haplotype in XPA combined ... BeFree 21751184 Detail
0.001 Non-small cell lung carcinoma Although smoking is the dominant risk factor of lung cancer, XPA -4G>A (rs180... BeFree 21195504 Detail
0.036 Malignant neoplasm of lung XPA gene rs1800975 single nucleotide polymorphism and lung cancer risk: a meta-a... BeFree 24696258 Detail
0.003 Carcinoma of lung XPA gene rs1800975 single nucleotide polymorphism and lung cancer risk: a meta-a... BeFree 24696258 Detail
0.006 Malignant neoplasm of breast Our findings provide clear evidence that XRCC1 gene rs25487 and XPA gene rs18009... BeFree 24642895 Detail
0.006 Malignant neoplasm of breast Moreover, the T-G (including rs2808668 and rs1800975) haplotype in XPA combined ... BeFree 21751184 Detail
<0.001 breast carcinoma Our findings provide clear evidence that XRCC1 gene rs25487 and XPA gene rs18009... BeFree 24642895 Detail
<0.001 breast carcinoma Moreover, the T-G (including rs2808668 and rs1800975) haplotype in XPA combined ... BeFree 21751184 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000380.4(XPA):c.-4A>G AND not specified ClinVar Detail
NM_000380.4(XPA):c.-4A>G AND Xeroderma pigmentosum group A ClinVar Detail
NM_000380.4(XPA):c.-4A>G AND not provided ClinVar Detail
Herein we performed a case-control study evaluating the influence of three single nucleotide polymor... DisGeNET Detail
Herein we performed a case-control study evaluating the influence of three single nucleotide polymor... DisGeNET Detail
Herein we performed a case-control study evaluating the influence of three single nucleotide polymor... DisGeNET Detail
Our findings provide clear evidence that XRCC1 gene rs25487 and XPA gene rs1800975 might exert both ... DisGeNET Detail
Moreover, the T-G (including rs2808668 and rs1800975) haplotype in XPA combined with the ERCC2 T all... DisGeNET Detail
Although smoking is the dominant risk factor of lung cancer, XPA -4G&gt;A (rs1800975) is also associ... DisGeNET Detail
Our findings provide clear evidence that XRCC1 gene rs25487 and XPA gene rs1800975 might exert both ... DisGeNET Detail
Moreover, the T-G (including rs2808668 and rs1800975) haplotype in XPA combined with the ERCC2 T all... DisGeNET Detail
Although smoking is the dominant risk factor of lung cancer, XPA -4G&gt;A (rs1800975) is also associ... DisGeNET Detail
XPA gene rs1800975 single nucleotide polymorphism and lung cancer risk: a meta-analysis. DisGeNET Detail
XPA gene rs1800975 single nucleotide polymorphism and lung cancer risk: a meta-analysis. DisGeNET Detail
Our findings provide clear evidence that XRCC1 gene rs25487 and XPA gene rs1800975 might exert both ... DisGeNET Detail
Moreover, the T-G (including rs2808668 and rs1800975) haplotype in XPA combined with the ERCC2 T all... DisGeNET Detail
Our findings provide clear evidence that XRCC1 gene rs25487 and XPA gene rs1800975 might exert both ... DisGeNET Detail
Moreover, the T-G (including rs2808668 and rs1800975) haplotype in XPA combined with the ERCC2 T all... 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
rs1800975 dbSNP
Genome
hg38
Position
chr9:97,697,296-97,697,296
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1152
Mean of sample read depth (HGVD)
41.09
Standard deviation of sample read depth (HGVD)
17.07
Number of reference allele (HGVD)
1146
Number of alternative allele (HGVD)
1158
Allele Frequency (HGVD)
0.5026041666666666
Gene Symbol (HGVD)
XPA
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))
rs1800975
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.505
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
8463
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Homozygous Counts (ExAC)
997
East Asian Chromosome Counts (ExAC)
8042
East Asian Allele Counts (ExAC)
4006
East Asian Heterozygous Counts (ExAC)
2012
East Asian Allele Frequency (ExAC)
0.49813479234021385
Chromosome Counts in All Race (ExAC)
109042
Allele Counts in All Race (ExAC)
69079
Heterozygous Counts in All Race (ExAC)
24688
Homozygous Counts in All Race (ExAC)
22195
Allele Frequency in All Race (ExAC)
0.6335081895049613
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