chr12-69755649-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022456.5(RAB3IP):āc.241T>Cā(p.Ser81Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000788 in 1,611,638 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
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.241T>C | p.Ser81Pro | missense_variant | 2/11 | ENST00000247833.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAB3IP | ENST00000247833.12 | c.241T>C | p.Ser81Pro | missense_variant | 2/11 | 1 | NM_022456.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000148 AC: 37AN: 250296Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135246
GnomAD4 exome AF: 0.0000774 AC: 113AN: 1459434Hom.: 0 Cov.: 30 AF XY: 0.0000813 AC XY: 59AN XY: 725766
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 03, 2022 | The c.289T>C (p.S97P) alteration is located in exon 2 (coding exon 2) of the RAB3IP gene. This alteration results from a T to C substitution at nucleotide position 289, causing the serine (S) at amino acid position 97 to be replaced by a proline (P). 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