rs1047840
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_130398.4(EXO1):c.1765G>A(p.Glu589Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 1,613,610 control chromosomes in the GnomAD database, including 116,572 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as 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 -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EXO1 | NM_130398.4 | c.1765G>A | p.Glu589Lys | missense_variant | 13/16 | ENST00000366548.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EXO1 | ENST00000366548.8 | c.1765G>A | p.Glu589Lys | missense_variant | 13/16 | 1 | NM_130398.4 | P2 | |
EXO1 | ENST00000348581.9 | c.1765G>A | p.Glu589Lys | missense_variant | 11/14 | 1 | P2 | ||
EXO1 | ENST00000518483.5 | c.1765G>A | p.Glu589Lys | missense_variant | 11/14 | 1 | A2 | ||
EXO1 | ENST00000521202.2 | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.399 AC: 60591AN: 151844Hom.: 12463 Cov.: 32
GnomAD3 exomes AF: 0.361 AC: 90738AN: 251400Hom.: 17062 AF XY: 0.356 AC XY: 48317AN XY: 135858
GnomAD4 exome AF: 0.374 AC: 546853AN: 1461648Hom.: 104070 Cov.: 39 AF XY: 0.371 AC XY: 270074AN XY: 727156
GnomAD4 genome ? AF: 0.399 AC: 60687AN: 151962Hom.: 12502 Cov.: 32 AF XY: 0.395 AC XY: 29352AN XY: 74282
ClinVar
Submissions by phenotype
EXO1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 18, 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