chr13-102875580-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000123.4(ERCC5):āc.3238G>Cā(p.Gly1080Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 1 in 1,613,176 control chromosomes in the GnomAD database, including 805,928 homozygotes. 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 Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G1080E) has been classified as Likely benign.
Frequency
Consequence
NM_000123.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERCC5 | NM_000123.4 | c.3238G>C | p.Gly1080Arg | missense_variant | 15/15 | ENST00000652225.2 | |
BIVM-ERCC5 | NM_001204425.2 | c.4600G>C | p.Gly1534Arg | missense_variant | 23/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERCC5 | ENST00000652225.2 | c.3238G>C | p.Gly1080Arg | missense_variant | 15/15 | NM_000123.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.998 AC: 151936AN: 152250Hom.: 75812 Cov.: 33
GnomAD3 exomes AF: 0.999 AC: 250311AN: 250462Hom.: 125080 AF XY: 0.999 AC XY: 135312AN XY: 135382
GnomAD4 exome AF: 1.00 AC: 1460458AN: 1460808Hom.: 730055 Cov.: 86 AF XY: 1.00 AC XY: 726510AN XY: 726676
GnomAD4 genome AF: 0.998 AC: 152056AN: 152368Hom.: 75873 Cov.: 33 AF XY: 0.998 AC XY: 74349AN XY: 74506
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
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