rs4150001
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_130398.4(EXO1):c.2276G>A(p.Gly759Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00869 in 1,613,746 control chromosomes in the GnomAD database, including 90 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_130398.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EXO1 | NM_130398.4 | c.2276G>A | p.Gly759Glu | missense_variant | 15/16 | ENST00000366548.8 | NP_569082.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EXO1 | ENST00000366548.8 | c.2276G>A | p.Gly759Glu | missense_variant | 15/16 | 1 | NM_130398.4 | ENSP00000355506.3 |
Frequencies
GnomAD3 genomes AF: 0.00813 AC: 1236AN: 151942Hom.: 12 Cov.: 32
GnomAD3 exomes AF: 0.00860 AC: 2161AN: 251200Hom.: 23 AF XY: 0.00842 AC XY: 1143AN XY: 135780
GnomAD4 exome AF: 0.00875 AC: 12791AN: 1461686Hom.: 78 Cov.: 32 AF XY: 0.00881 AC XY: 6405AN XY: 727154
GnomAD4 genome AF: 0.00813 AC: 1237AN: 152060Hom.: 12 Cov.: 32 AF XY: 0.00861 AC XY: 640AN XY: 74336
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | EXO1: BP4, BS2 - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 13, 2018 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 16, 2016 | - - |
EXO1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | May 09, 2019 | This variant is classified as likely 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