rs144455066
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_012233.3(RAB3GAP1):c.2676G>T(p.Arg892Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000563 in 1,612,968 control chromosomes in the GnomAD database, including 4 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_012233.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAB3GAP1 | NM_012233.3 | c.2676G>T | p.Arg892Ser | missense_variant | 23/24 | ENST00000264158.13 | NP_036365.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAB3GAP1 | ENST00000264158.13 | c.2676G>T | p.Arg892Ser | missense_variant | 23/24 | 1 | NM_012233.3 | ENSP00000264158.8 |
Frequencies
GnomAD3 genomes AF: 0.00276 AC: 420AN: 152116Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000785 AC: 197AN: 250994Hom.: 1 AF XY: 0.000531 AC XY: 72AN XY: 135658
GnomAD4 exome AF: 0.000334 AC: 488AN: 1460734Hom.: 3 Cov.: 31 AF XY: 0.000282 AC XY: 205AN XY: 726732
GnomAD4 genome AF: 0.00276 AC: 420AN: 152234Hom.: 1 Cov.: 32 AF XY: 0.00270 AC XY: 201AN XY: 74428
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 26, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 29, 2017 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 21, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 20, 2019 | - - |
RAB3GAP1-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | May 08, 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