rs9514066
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_000123.4(ERCC5):c.3157G>A(p.Gly1053Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Benignin Lovd.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ERCC5
NM_000123.4 missense
NM_000123.4 missense
Scores
3
15
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.47
Genes affected
ERCC5 (HGNC:3437): (ERCC excision repair 5, endonuclease) This gene encodes a single-strand specific DNA endonuclease that makes the 3' incision in DNA excision repair following UV-induced damage. The protein may also function in other cellular processes, including RNA polymerase II transcription, and transcription-coupled DNA repair. Mutations in this gene cause xeroderma pigmentosum complementation group G (XP-G), which is also referred to as xeroderma pigmentosum VII (XP7), a skin disorder characterized by hypersensitivity to UV light and increased susceptibility for skin cancer development following UV exposure. Some patients also develop Cockayne syndrome, which is characterized by severe growth defects, cognitive disability, and cachexia. Read-through transcription exists between this gene and the neighboring upstream BIVM (basic, immunoglobulin-like variable motif containing) gene. [provided by RefSeq, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.14782965).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ERCC5 | NM_000123.4 | c.3157G>A | p.Gly1053Arg | missense_variant | 15/15 | ENST00000652225.2 | NP_000114.3 | |
BIVM-ERCC5 | NM_001204425.2 | c.4519G>A | p.Gly1507Arg | missense_variant | 23/23 | NP_001191354.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ERCC5 | ENST00000652225.2 | c.3157G>A | p.Gly1053Arg | missense_variant | 15/15 | NM_000123.4 | ENSP00000498881 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152198Hom.: 0 Cov.: 31 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1461882Hom.: 0 Cov.: 95 AF XY: 0.00 AC XY: 0AN XY: 727244
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GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152198Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74332
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;.;.;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T;.;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;.;.;M;.
MutationTaster
Benign
N;N
PROVEAN
Benign
.;.;.;N;N
REVEL
Benign
Sift
Benign
.;.;.;D;T
Sift4G
Uncertain
.;.;.;D;T
Polyphen
0.93
.;.;.;P;.
Vest4
0.079, 0.12
MutPred
0.34
.;.;.;Gain of MoRF binding (P = 0.0246);.;
MVP
0.37
MPC
0.51
ClinPred
D
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at