1-220196404-A-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_012414.4(RAB3GAP2):c.812-6T>A 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 0.000241 in 452,568 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAB3GAP2 | NM_012414.4 | c.812-6T>A | 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.812-6T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_012414.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000124 AC: 10AN: 80754Hom.: 0 Cov.: 21
GnomAD3 exomes AF: 0.000108 AC: 19AN: 176608Hom.: 0 AF XY: 0.0000740 AC XY: 7AN XY: 94616
GnomAD4 exome AF: 0.000266 AC: 99AN: 371810Hom.: 0 Cov.: 0 AF XY: 0.000279 AC XY: 52AN XY: 186482
GnomAD4 genome AF: 0.000124 AC: 10AN: 80758Hom.: 0 Cov.: 21 AF XY: 0.000154 AC XY: 6AN XY: 38908
ClinVar
Submissions by phenotype
Martsolf syndrome;C3280214:Warburg micro syndrome 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at