rs458017
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBA1
The NM_001372078.1(REV3L):c.3467A>G(p.Tyr1156Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0613 in 1,613,740 control chromosomes in the GnomAD database, including 3,293 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 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_001372078.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
REV3L | NM_001372078.1 | c.3467A>G | p.Tyr1156Cys | missense_variant | 13/32 | ENST00000368802.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
REV3L | ENST00000368802.8 | c.3467A>G | p.Tyr1156Cys | missense_variant | 13/32 | 1 | NM_001372078.1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0561 AC: 8537AN: 152140Hom.: 272 Cov.: 32
GnomAD3 exomes AF: 0.0593 AC: 14855AN: 250414Hom.: 518 AF XY: 0.0598 AC XY: 8097AN XY: 135480
GnomAD4 exome AF: 0.0618 AC: 90370AN: 1461482Hom.: 3022 Cov.: 45 AF XY: 0.0619 AC XY: 44974AN XY: 727018
GnomAD4 genome ? AF: 0.0561 AC: 8539AN: 152258Hom.: 271 Cov.: 32 AF XY: 0.0542 AC XY: 4038AN XY: 74452
ClinVar
Submissions by phenotype
REV3L-related condition Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 01, 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