12-69801696-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_022456.5(RAB3IP):c.1105T>G(p.Ser369Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000959 in 1,460,406 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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 Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAB3IP | NM_022456.5 | c.1105T>G | p.Ser369Ala | missense_variant | 8/11 | ENST00000247833.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAB3IP | ENST00000247833.12 | c.1105T>G | p.Ser369Ala | missense_variant | 8/11 | 1 | NM_022456.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 28
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251040Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135678
GnomAD4 exome AF: 0.00000959 AC: 14AN: 1460406Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 726530
GnomAD4 genome ? Cov.: 28
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 04, 2023 | The c.1153T>G (p.S385A) alteration is located in exon 8 (coding exon 8) of the RAB3IP gene. This alteration results from a T to G substitution at nucleotide position 1153, causing the serine (S) at amino acid position 385 to be replaced by an alanine (A). 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