rs74477879
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000259698.9(RIPOR2):āc.1146C>Gā(p.Phe382Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00531 in 1,551,674 control chromosomes in the GnomAD database, including 220 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
ENST00000259698.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RIPOR2 | NM_001286445.3 | c.1164+402C>G | intron_variant | ENST00000643898.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RIPOR2 | ENST00000643898.2 | c.1164+402C>G | intron_variant | NM_001286445.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0214 AC: 3254AN: 152196Hom.: 123 Cov.: 32
GnomAD3 exomes AF: 0.00515 AC: 805AN: 156436Hom.: 15 AF XY: 0.00438 AC XY: 363AN XY: 82874
GnomAD4 exome AF: 0.00356 AC: 4980AN: 1399360Hom.: 95 Cov.: 31 AF XY: 0.00322 AC XY: 2223AN XY: 690188
GnomAD4 genome ? AF: 0.0214 AC: 3261AN: 152314Hom.: 125 Cov.: 32 AF XY: 0.0198 AC XY: 1477AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 24, 2018 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 23, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at