rs9358802

Variant names:

• chr6-24818557-A-C
• rs9358802
• NM_001286445.3:c.2937T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-24818557-A-C
• chr6-24818557-A-G
• chr6-24818557-A-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730

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]

ACMG classification

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
RIPOR2	NM_001286445.3	c.2937T>G	p.Ala979Ala	synonymous_variant	Exon 20 of 22	ENST00000643898.2	NP_001273374.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RIPOR2	ENST00000643898.2	c.2937T>G	p.Ala979Ala	synonymous_variant	Exon 20 of 22		NM_001286445.3	ENSP00000494268.2
RIPOR2	ENST00000259698.9	c.3000T>G	p.Ala1000Ala	synonymous_variant	Exon 21 of 23	1		ENSP00000259698.4
RIPOR2	ENST00000613507.4	c.3000T>G	p.Ala1000Ala	synonymous_variant	Exon 21 of 23	5		ENSP00000482957.1
RIPOR2	ENST00000538035.6	c.2850T>G	p.Ala950Ala	synonymous_variant	Exon 20 of 22	2		ENSP00000441138.2

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

Other links and lift over

dbSNP: rs9358802; hg19: chr6-24818785;