chr16:13948101:T>C Detail (hg38) (ERCC4)

Information

Genome

Assembly Position
hg19 chr16:14,041,958-14,041,958 View the variant detail on this assembly version.
hg38 chr16:13,948,101-13,948,101

HGVS

Type Transcript Protein
RefSeq NM_005236.2:c.2505T>C NP_005227.1:p.Ser835=
Ensemble ENST00000311895.8:c.2505T>C ENST00000311895.8:p.Ser835=
ENST00000682617.1:c.2643T>C ENST00000682617.1:p.Ser881=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.251
ToMMo:0.241
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.235

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 133520 OMIM
HGNC 3436 HGNC
Ensembl ENSG00000175595 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv54823739 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign criteria provided, single submitter not specified germline Detail
Benign 2023-07-07 criteria provided, multiple submitters, no conflicts Xeroderma pigmentosum, group F germline Detail
Benign 2024-02-01 criteria provided, single submitter Fanconi anemia complementation group Q,Cockayne syndrome,Xeroderma pigmentosum, group F germline Detail
Benign 2024-02-01 criteria provided, single submitter Fanconi anemia complementation group Q,Cockayne syndrome,Xeroderma pigmentosum, group F germline Detail
Benign 2024-02-01 criteria provided, single submitter Fanconi anemia complementation group Q,Cockayne syndrome,Xeroderma pigmentosum, group F germline Detail
Benign 2019-02-26 criteria provided, single submitter not provided germline Detail
Benign 2021-07-30 criteria provided, single submitter XFE progeroid syndrome germline Detail
Benign 2021-07-30 criteria provided, single submitter Fanconi anemia complementation group Q germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Squamous cell carcinoma of oropharynx Our findings suggest that the ERCC4 T2505C polymorphism may be associated with i... BeFree 15936543 Detail
0.005 breast carcinoma We evaluated associations between seven single-nucleotide polymorphisms in four ... BeFree 21622940 Detail
0.018 breast carcinoma We evaluated associations between seven single-nucleotide polymorphisms in four ... BeFree 21622940 Detail
0.098 Malignant neoplasm of breast We evaluated associations between seven single-nucleotide polymorphisms in four ... BeFree 21622940 Detail
0.002 breast carcinoma We evaluated associations between seven single-nucleotide polymorphisms in four ... BeFree 21622940 Detail
0.026 Malignant neoplasm of breast We evaluated associations between seven single-nucleotide polymorphisms in four ... BeFree 21622940 Detail
0.023 Malignant neoplasm of breast We evaluated associations between seven single-nucleotide polymorphisms in four ... BeFree 21622940 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_005236.3(ERCC4):c.2505T>C (p.Ser835=) AND not specified ClinVar Detail
NM_005236.3(ERCC4):c.2505T>C (p.Ser835=) AND Xeroderma pigmentosum, group F ClinVar Detail
NM_005236.3(ERCC4):c.2505T>C (p.Ser835=) AND multiple conditions ClinVar Detail
NM_005236.3(ERCC4):c.2505T>C (p.Ser835=) AND multiple conditions ClinVar Detail
NM_005236.3(ERCC4):c.2505T>C (p.Ser835=) AND multiple conditions ClinVar Detail
NM_005236.3(ERCC4):c.2505T>C (p.Ser835=) AND not provided ClinVar Detail
NM_005236.3(ERCC4):c.2505T>C (p.Ser835=) AND XFE progeroid syndrome ClinVar Detail
NM_005236.3(ERCC4):c.2505T>C (p.Ser835=) AND Fanconi anemia complementation group Q ClinVar Detail
Our findings suggest that the ERCC4 T2505C polymorphism may be associated with improved recovery fro... DisGeNET Detail
We evaluated associations between seven single-nucleotide polymorphisms in four DNA repair genes (ER... DisGeNET Detail
We evaluated associations between seven single-nucleotide polymorphisms in four DNA repair genes (ER... DisGeNET Detail
We evaluated associations between seven single-nucleotide polymorphisms in four DNA repair genes (ER... DisGeNET Detail
We evaluated associations between seven single-nucleotide polymorphisms in four DNA repair genes (ER... DisGeNET Detail
We evaluated associations between seven single-nucleotide polymorphisms in four DNA repair genes (ER... DisGeNET Detail
We evaluated associations between seven single-nucleotide polymorphisms in four DNA repair genes (ER... 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
rs1799801 dbSNP
Genome
hg38
Position
chr16:13,948,101-13,948,101
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
153.49
Standard deviation of sample read depth (HGVD)
70.98
Number of reference allele (HGVD)
1812
Number of alternative allele (HGVD)
608
Allele Frequency (HGVD)
0.2512396694214876
Gene Symbol (HGVD)
ERCC4
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))
rs1799801
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2405
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4030
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8612
East Asian Allele Counts (ExAC)
2026
East Asian Heterozygous Counts (ExAC)
1576
East Asian Homozygous Counts (ExAC)
225
East Asian Allele Frequency (ExAC)
0.23525313516024152
Chromosome Counts in All Race (ExAC)
121226
Allele Counts in All Race (ExAC)
33007
Heterozygous Counts in All Race (ExAC)
23795
Homozygous Counts in All Race (ExAC)
4606
Allele Frequency in All Race (ExAC)
0.27227657433223895
Genome browser