chr6-24894191-G-A

Variant names:

• chr6-24894191-G-A
• rs734015
• NM_001286445.3:c.62-18374C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001286445.3(RIPOR2):​c.62-18374C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,060 control chromosomes in the GnomAD database, including 14,129 homozygotes. 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: 𝑓 0.42 (14129 hom., cov: 32)
• Consequence: RIPOR2 NM_001286445.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.295
• Publications: 1 publications found

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]

RIPOR2 Gene-Disease associations (from GenCC):

• autosomal recessive nonsyndromic hearing loss 104

  Inheritance: AR Classification: MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, PanelApp Australia
• nonsyndromic genetic hearing loss

  Inheritance: AR Classification: MODERATE Submitted by: ClinGen
• hearing loss, autosomal recessive

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• autosomal dominant nonsyndromic hearing loss 21

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001286445.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RIPOR2	NM_001286445.3	MANE Select	c.62-18374C>T		intron	N/A	NP_001273374.1
	RIPOR2	NM_014722.5		c.-27+16627C>T		intron	N/A	NP_055537.2
	RIPOR2	NM_001346031.2		c.-27+16627C>T		intron	N/A	NP_001332960.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RIPOR2	ENST00000643898.2	MANE Select	c.62-18374C>T		intron	N/A	ENSP00000494268.2
	RIPOR2	ENST00000259698.9	TSL:1	c.-27+16627C>T		intron	N/A	ENSP00000259698.4
	RIPOR2	ENST00000613507.4	TSL:5	c.-26-18374C>T		intron	N/A	ENSP00000482957.1

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64469 AN: 151942 Hom.: 14113 Cov.: 32

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.405

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.424 AC: 64522 AN: 152060 Hom.: 14129 Cov.: 32 AF XY: 0.419 AC XY: 31128 AN XY: 74324

African (AFR) AF: 0.503 AC: 20867 AN: 41476

American (AMR) AF: 0.403 AC: 6158 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 974 AN: 3466

East Asian (EAS) AF: 0.271 AC: 1403 AN: 5172

South Asian (SAS) AF: 0.476 AC: 2292 AN: 4816

European-Finnish (FIN) AF: 0.331 AC: 3504 AN: 10574

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27955 AN: 67964

Other (OTH) AF: 0.402 AC: 849 AN: 2110

Alfa AF: 0.409 Hom.: 5585

Bravo AF: 0.426

Asia WGS AF: 0.378 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.9
DANN	Benign	0.37
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs734015; hg19: chr6-24894419;