chr12-69756446-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022456.5(RAB3IP):c.293T>A(p.Val98Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000855 in 1,613,904 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022456.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAB3IP | NM_022456.5 | c.293T>A | p.Val98Asp | missense_variant | 3/11 | ENST00000247833.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAB3IP | ENST00000247833.12 | c.293T>A | p.Val98Asp | missense_variant | 3/11 | 1 | NM_022456.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152124Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000143 AC: 36AN: 251382Hom.: 0 AF XY: 0.000147 AC XY: 20AN XY: 135882
GnomAD4 exome AF: 0.0000807 AC: 118AN: 1461780Hom.: 0 Cov.: 31 AF XY: 0.0000839 AC XY: 61AN XY: 727188
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152124Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 01, 2023 | The c.341T>A (p.V114D) alteration is located in exon 3 (coding exon 3) of the RAB3IP gene. This alteration results from a T to A substitution at nucleotide position 341, causing the valine (V) at amino acid position 114 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at