rs462779
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBA1
The NM_001372078.1(REV3L):c.3671C>T(p.Thr1224Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 1,612,660 control chromosomes in the GnomAD database, including 486,868 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 (★). 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.3671C>T | p.Thr1224Ile | missense_variant | 13/32 | ENST00000368802.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
REV3L | ENST00000368802.8 | c.3671C>T | p.Thr1224Ile | missense_variant | 13/32 | 1 | NM_001372078.1 | P4 |
Frequencies
GnomAD3 genomes AF: 0.673 AC: 102206AN: 151876Hom.: 36556 Cov.: 31
GnomAD3 exomes AF: 0.718 AC: 179543AN: 250086Hom.: 66509 AF XY: 0.730 AC XY: 98834AN XY: 135398
GnomAD4 exome AF: 0.779 AC: 1137992AN: 1460666Hom.: 450304 Cov.: 52 AF XY: 0.779 AC XY: 566158AN XY: 726634
GnomAD4 genome AF: 0.673 AC: 102260AN: 151994Hom.: 36564 Cov.: 31 AF XY: 0.668 AC XY: 49639AN XY: 74288
ClinVar
Submissions by phenotype
REV3L-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 06, 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