2-135168631-AC-A
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PVS1_ModeratePM2PP5
The NM_012233.3(RAB3GAP1):c.2801del(p.Pro934LeufsTer87) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,613,776 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. P933P) has been classified as Likely benign.
Frequency
Consequence
NM_012233.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAB3GAP1 | NM_012233.3 | c.2801del | p.Pro934LeufsTer87 | frameshift_variant | 24/24 | ENST00000264158.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAB3GAP1 | ENST00000264158.13 | c.2801del | p.Pro934LeufsTer87 | frameshift_variant | 24/24 | 1 | NM_012233.3 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151886Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251404Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135868
GnomAD4 exome AF: 0.0000239 AC: 35AN: 1461890Hom.: 0 Cov.: 32 AF XY: 0.0000275 AC XY: 20AN XY: 727248
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151886Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74188
ClinVar
Submissions by phenotype
Warburg micro syndrome 1 Pathogenic:1Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 01, 2005 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at