NM_002900.3:c.2650G>A

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_002900.3(RBP3):c.2650G>A(p.Val884Met) variant causes a missense change. The variant allele was found at a frequency of 0.0023 in 1,613,042 control chromosomes in the GnomAD database, including 49 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0032 ( 12 hom., cov: 33)

Exomes 𝑓: 0.0022 ( 37 hom. )

Consequence

RBP3
NM_002900.3 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 3.86

Variant links:

Genes affected

RBP3 (HGNC:9921): (retinol binding protein 3) Interphotoreceptor retinol-binding protein is a large glycoprotein known to bind retinoids and found primarily in the interphotoreceptor matrix of the retina between the retinal pigment epithelium and the photoreceptor cells. It is thought to transport retinoids between the retinal pigment epithelium and the photoreceptors, a critical role in the visual process.The human IRBP gene is approximately 9.5 kbp in length and consists of four exons separated by three introns. The introns are 1.6-1.9 kbp long. The gene is transcribed by photoreceptor and retinoblastoma cells into an approximately 4.3-kilobase mRNA that is translated and processed into a glycosylated protein of 135,000 Da. The amino acid sequence of human IRBP can be divided into four contiguous homology domains with 33-38% identity, suggesting a series of gene duplication events. In the gene, the boundaries of these domains are not defined by exon-intron junctions, as might have been expected. The first three homology domains and part of the fourth are all encoded by the first large exon, which is 3,180 base pairs long. The remainder of the fourth domain is encoded in the last three exons, which are 191, 143, and approximately 740 base pairs long, respectively. [provided by RefSeq, Jul 2008]

RBP3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.014441848).

BP6

Variant 10-47351134-G-A is Benign according to our data. Variant chr10-47351134-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 193238.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-47351134-G-A is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00316 (481/152392) while in subpopulation EAS AF= 0.0477 (247/5182). AF 95% confidence interval is 0.0428. There are 12 homozygotes in gnomad4. There are 280 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 12 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBP3	NM_002900.3 link	c.2650G>A	p.Val884Met	missense_variant	Exon 1 of 4	ENST00000584701.2	NP_002891.1	P10745

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBP3	ENST00000584701.2 link	c.2650G>A	p.Val884Met	missense_variant	Exon 1 of 4	1	NM_002900.3	ENSP00000463151.1		P10745

Frequencies

GnomAD3 genomes

AF:

0.00316

AC:

481

AN:

152274

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000506

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00582

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.0477

Gnomad SAS

AF:

0.00434

Gnomad FIN

AF:

0.00470

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000647

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00678

AC:

1689

AN:

249218

Hom.:

AF XY:

0.00617

AC XY:

836

AN XY:

135386

show subpopulations

Gnomad AFR exome

AF:

0.000313

Gnomad AMR exome

AF:

0.0146

Gnomad ASJ exome

AF:

0.00190

Gnomad EAS exome

AF:

0.0440

Gnomad SAS exome

AF:

0.00222

Gnomad FIN exome

AF:

0.00852

Gnomad NFE exome

AF:

0.000695

Gnomad OTH exome

AF:

0.00394

GnomAD4 exome

AF:

0.00221

AC:

3228

AN:

1460650

Hom.:

Cov.:

AF XY:

0.00218

AC XY:

1581

AN XY:

726632

show subpopulations

Gnomad4 AFR exome

AF:

0.000239

Gnomad4 AMR exome

AF:

0.0138

Gnomad4 ASJ exome

AF:

0.00226

Gnomad4 EAS exome

AF:

0.0332

Gnomad4 SAS exome

AF:

0.00283

Gnomad4 FIN exome

AF:

0.00699

Gnomad4 NFE exome

AF:

0.000341

Gnomad4 OTH exome

AF:

0.00384

GnomAD4 genome

AF:

0.00316

AC:

481

AN:

152392

Hom.:

Cov.:

AF XY:

0.00376

AC XY:

280

AN XY:

74528

show subpopulations

Gnomad4 AFR

AF:

0.000505

Gnomad4 AMR

AF:

0.00588

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.0477

Gnomad4 SAS

AF:

0.00434

Gnomad4 FIN

AF:

0.00470

Gnomad4 NFE

AF:

0.000647

Gnomad4 OTH

AF:

0.00236

Alfa

AF:

0.000875

Hom.:

Bravo

AF:

0.00398

Asia WGS

AF:

0.0170

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Retinitis pigmentosa;C3715216:Retinitis pigmentosa 66

Benign:1

May 17, 2022

Fulgent Genetics, Fulgent Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

Jan 28, 2015

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Retinal dystrophy

Benign:1

Oct 01, 2023

Dept Of Ophthalmology, Nagoya University

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: research

- -

Retinitis pigmentosa

Benign:1

Apr 27, 2017

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.23

BayesDel_noAF

Pathogenic

0.17

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.12

LIST_S2

Uncertain

0.90

MetaRNN

Benign

0.014

Sift4G

Uncertain

0.0040

Vest4

0.51

gMVP

0.92

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over