rs35396665
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP6_Very_Strong
The NM_012414.4(RAB3GAP2):c.812-7_812-6del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00052 in 1,342,468 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_012414.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAB3GAP2 | NM_012414.4 | c.812-7_812-6del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000358951.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAB3GAP2 | ENST00000358951.7 | c.812-7_812-6del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_012414.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000686 AC: 10AN: 145680Hom.: 0 Cov.: 21
GnomAD4 exome AF: 0.000575 AC: 688AN: 1196726Hom.: 0 AF XY: 0.000525 AC XY: 314AN XY: 597972
GnomAD4 genome ? AF: 0.0000686 AC: 10AN: 145742Hom.: 0 Cov.: 21 AF XY: 0.0000565 AC XY: 4AN XY: 70832
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Aug 26, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | RAB3GAP2: BP4 - |
Martsolf syndrome;C3280214:Warburg micro syndrome 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at