chr10:49470671:T>C Detail (hg38) (ERCC6)

Information

Genome

Assembly Position
hg19 chr10:50,678,717-50,678,717 View the variant detail on this assembly version.
hg38 chr10:49,470,671-49,470,671

HGVS

Type Transcript Protein
RefSeq NM_000124.3:c.3289A>G NP_000115.1:p.Met1097Val
Ensemble ENST00000355832.10:c.3289A>G ENST00000355832.10:p.Met1097Val
ENST00000681659.1:c.3130A>G ENST00000681659.1:p.Met1044Val
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.058
ToMMo:0.051
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.052

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 609413 OMIM
HGNC 3438 HGNC
Ensembl ENSG00000225830 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv39227951 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign Likely benign 2021-12-03 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2016-06-14 criteria provided, single submitter Cockayne syndrome germline Detail
Benign 2016-06-14 criteria provided, single submitter COFS syndrome germline Detail
Benign 2016-06-14 criteria provided, single submitter macular degeneration germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.004 breast carcinoma In a nested case-control study of breast cancer in US radiologic technologists e... BeFree 18767034 Detail
<0.001 breast carcinoma In a nested case-control study of breast cancer in US radiologic technologists e... BeFree 18767034 Detail
0.032 Malignant neoplasm of breast In a nested case-control study of breast cancer in US radiologic technologists e... BeFree 18767034 Detail
0.010 Malignant neoplasm of breast In a nested case-control study of breast cancer in US radiologic technologists e... BeFree 18767034 Detail
0.001 Carcinoma of bladder In classification and regression tree analysis, we observed gene-gene interactio... BeFree 17728339 Detail
0.015 Malignant neoplasm of urinary bladder In classification and regression tree analysis, we observed gene-gene interactio... BeFree 17728339 Detail
0.005 Malignant neoplasm of urinary bladder In classification and regression tree analysis, we observed gene-gene interactio... BeFree 17728339 Detail
<0.001 Carcinoma of bladder In classification and regression tree analysis, we observed gene-gene interactio... BeFree 17728339 Detail
0.003 Malignant neoplasm of prostate In conclusion, we found that polymorphisms in XPG rs2296147 and CSB rs2228526 we... BeFree 24615090 Detail
0.002 prostate carcinoma In conclusion, we found that polymorphisms in XPG rs2296147 and CSB rs2228526 we... BeFree 24615090 Detail
<0.001 prostate carcinoma In conclusion, we found that polymorphisms in XPG rs2296147 and CSB rs2228526 we... BeFree 24615090 Detail
<0.001 prostate carcinoma Our study indicates that XPG rs2296147 and CSB rs2228526 polymorphisms are signi... BeFree 24289586 Detail
0.004 Malignant neoplasm of prostate In conclusion, we found that polymorphisms in XPG rs2296147 and CSB rs2228526 we... BeFree 24615090 Detail
0.004 Malignant neoplasm of prostate Our study indicates that XPG rs2296147 and CSB rs2228526 polymorphisms are signi... BeFree 24289586 Detail
0.003 Malignant neoplasm of prostate Our study indicates that XPG rs2296147 and CSB rs2228526 polymorphisms are signi... BeFree 24289586 Detail
0.002 prostate carcinoma Our study indicates that XPG rs2296147 and CSB rs2228526 polymorphisms are signi... BeFree 24289586 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000124.4(ERCC6):c.3289A>G (p.Met1097Val) AND not specified ClinVar Detail
NM_000124.4(ERCC6):c.3289A>G (p.Met1097Val) AND Cockayne syndrome ClinVar Detail
NM_000124.4(ERCC6):c.3289A>G (p.Met1097Val) AND COFS syndrome ClinVar Detail
NM_000124.4(ERCC6):c.3289A>G (p.Met1097Val) AND Macular degeneration ClinVar Detail
NM_000124.4(ERCC6):c.3289A>G (p.Met1097Val) AND not provided ClinVar Detail
In a nested case-control study of breast cancer in US radiologic technologists exposed to low levels... DisGeNET Detail
In a nested case-control study of breast cancer in US radiologic technologists exposed to low levels... DisGeNET Detail
In a nested case-control study of breast cancer in US radiologic technologists exposed to low levels... DisGeNET Detail
In a nested case-control study of breast cancer in US radiologic technologists exposed to low levels... DisGeNET Detail
In classification and regression tree analysis, we observed gene-gene interactions among CCNH V270A,... DisGeNET Detail
In classification and regression tree analysis, we observed gene-gene interactions among CCNH V270A,... DisGeNET Detail
In classification and regression tree analysis, we observed gene-gene interactions among CCNH V270A,... DisGeNET Detail
In classification and regression tree analysis, we observed gene-gene interactions among CCNH V270A,... DisGeNET Detail
In conclusion, we found that polymorphisms in XPG rs2296147 and CSB rs2228526 were significantly ass... DisGeNET Detail
In conclusion, we found that polymorphisms in XPG rs2296147 and CSB rs2228526 were significantly ass... DisGeNET Detail
In conclusion, we found that polymorphisms in XPG rs2296147 and CSB rs2228526 were significantly ass... DisGeNET Detail
Our study indicates that XPG rs2296147 and CSB rs2228526 polymorphisms are significantly associated ... DisGeNET Detail
In conclusion, we found that polymorphisms in XPG rs2296147 and CSB rs2228526 were significantly ass... DisGeNET Detail
Our study indicates that XPG rs2296147 and CSB rs2228526 polymorphisms are significantly associated ... DisGeNET Detail
Our study indicates that XPG rs2296147 and CSB rs2228526 polymorphisms are significantly associated ... DisGeNET Detail
Our study indicates that XPG rs2296147 and CSB rs2228526 polymorphisms are significantly associated ... 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
rs2228526 dbSNP
Genome
hg38
Position
chr10:49,470,671-49,470,671
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
204.11
Standard deviation of sample read depth (HGVD)
92.82
Number of reference allele (HGVD)
2279
Number of alternative allele (HGVD)
141
Allele Frequency (HGVD)
0.05826446280991736
Gene Symbol (HGVD)
ERCC6
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))
rs2228526
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0511
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
857
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)
451
East Asian Heterozygous Counts (ExAC)
423
East Asian Homozygous Counts (ExAC)
14
East Asian Allele Frequency (ExAC)
0.05211462907326092
Chromosome Counts in All Race (ExAC)
121374
Allele Counts in All Race (ExAC)
26527
Heterozygous Counts in All Race (ExAC)
19941
Homozygous Counts in All Race (ExAC)
3293
Allele Frequency in All Race (ExAC)
0.2185558686374347
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