9-95876046-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_020207.7(ERCC6L2):c.8C>A(p.Pro3Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00877 in 1,588,756 control chromosomes in the GnomAD database, including 78 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P3L) has been classified as Uncertain significance.
Frequency
Consequence
NM_020207.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERCC6L2 | NM_020207.7 | c.8C>A | p.Pro3Gln | missense_variant | 1/19 | ENST00000653738.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERCC6L2 | ENST00000653738.2 | c.8C>A | p.Pro3Gln | missense_variant | 1/19 | NM_020207.7 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00614 AC: 935AN: 152228Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00618 AC: 1261AN: 203882Hom.: 8 AF XY: 0.00581 AC XY: 645AN XY: 110928
GnomAD4 exome AF: 0.00905 AC: 13006AN: 1436410Hom.: 72 Cov.: 32 AF XY: 0.00857 AC XY: 6106AN XY: 712436
GnomAD4 genome AF: 0.00614 AC: 935AN: 152346Hom.: 6 Cov.: 32 AF XY: 0.00609 AC XY: 454AN XY: 74500
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | ERCC6L2: BP4, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 21, 2021 | - - |
ERCC6L2-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 30, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at