rs61741706
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001286445.3(RIPOR2):c.2581G>A(p.Val861Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00648 in 1,551,306 control chromosomes in the GnomAD database, including 226 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. V861V) has been classified as Likely benign.
Frequency
Consequence
NM_001286445.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.2581G>A | p.Val861Ile | missense_variant | 18/22 | ENST00000643898.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RIPOR2 | ENST00000643898.2 | c.2581G>A | p.Val861Ile | missense_variant | 18/22 | NM_001286445.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0227 AC: 3452AN: 152100Hom.: 123 Cov.: 32
GnomAD3 exomes AF: 0.00678 AC: 1059AN: 156134Hom.: 19 AF XY: 0.00621 AC XY: 514AN XY: 82752
GnomAD4 exome AF: 0.00471 AC: 6589AN: 1399088Hom.: 101 Cov.: 31 AF XY: 0.00449 AC XY: 3098AN XY: 690046
GnomAD4 genome ? AF: 0.0227 AC: 3459AN: 152218Hom.: 125 Cov.: 32 AF XY: 0.0213 AC XY: 1585AN XY: 74414
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Aug 23, 2017 | p.Val882Ile in exon 19 of FAM65B: This variant is not expected to have clinical significance because it has been identified in 7.48% (159/2126) of African chrom osomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org ; dbSNP rs61741706). - |
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. - |
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 | - - |
RIPOR2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 26, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at