rs4150387
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000123.4(ERCC5):c.3026G>A(p.Arg1009His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000117 in 1,613,868 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1009C) has been classified as Uncertain significance.
Frequency
Consequence
NM_000123.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERCC5 | NM_000123.4 | c.3026G>A | p.Arg1009His | missense_variant | 15/15 | ENST00000652225.2 | |
BIVM-ERCC5 | NM_001204425.2 | c.4388G>A | p.Arg1463His | missense_variant | 23/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERCC5 | ENST00000652225.2 | c.3026G>A | p.Arg1009His | missense_variant | 15/15 | NM_000123.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000454 AC: 69AN: 152080Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000171 AC: 43AN: 251248Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135798
GnomAD4 exome AF: 0.0000821 AC: 120AN: 1461670Hom.: 0 Cov.: 30 AF XY: 0.0000564 AC XY: 41AN XY: 727148
GnomAD4 genome ? AF: 0.000453 AC: 69AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.000457 AC XY: 34AN XY: 74392
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | curation | Sema4, Sema4 | Dec 13, 2021 | - - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at