NM_001286445.3:c.2937T>G

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_001286445.3(RIPOR2):​c.2937T>G​(p.Ala979Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 30)

Consequence

RIPOR2
NM_001286445.3 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0730
Variant links:
Genes affected
RIPOR2 (HGNC:13872): (RHO family interacting cell polarization regulator 2) This gene encodes an atypical inhibitor of the small G protein RhoA. Inhibition of RhoA activity by the encoded protein mediates myoblast fusion and polarization of T cells and neutrophils. The encoded protein is a component of hair cell stereocilia that is essential for hearing. A splice site mutation in this gene results in hearing loss in human patients. [provided by RefSeq, Sep 2016]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP7
Synonymous conserved (PhyloP=-0.073 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RIPOR2NM_001286445.3 linkc.2937T>G p.Ala979Ala synonymous_variant Exon 20 of 22 ENST00000643898.2 NP_001273374.1 A0A2R8YEE0B7Z5J9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RIPOR2ENST00000643898.2 linkc.2937T>G p.Ala979Ala synonymous_variant Exon 20 of 22 NM_001286445.3 ENSP00000494268.2 A0A2R8YEE0
RIPOR2ENST00000259698.9 linkc.3000T>G p.Ala1000Ala synonymous_variant Exon 21 of 23 1 ENSP00000259698.4 Q9Y4F9-1
RIPOR2ENST00000613507.4 linkc.3000T>G p.Ala1000Ala synonymous_variant Exon 21 of 23 5 ENSP00000482957.1 Q9Y4F9-1
RIPOR2ENST00000538035.6 linkc.2850T>G p.Ala950Ala synonymous_variant Exon 20 of 22 2 ENSP00000441138.2 F5GX51

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.67
CADD
Benign
7.3
DANN
Benign
0.59

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9358802; hg19: chr6-24818785; API