Variant 19-32676302-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_207391.3(RGS9BP):c.39C>G(p.Leu13Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0432 in 1,607,320 control chromosomes in the GnomAD database, including 2,453 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.041 ( 226 hom., cov: 34)

Exomes 𝑓: 0.043 ( 2227 hom. )

Consequence

RGS9BP
NM_207391.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 2.88

Variant links:

Genes affected

RGS9BP (HGNC:30304): (regulator of G protein signaling 9 binding protein) The protein encoded by this gene functions as a regulator of G protein-coupled receptor signaling in phototransduction. Studies in bovine and mouse show that this gene is expressed only in the retina, and is localized in the rod outer segment membranes. This protein is associated with a heterotetrameric complex, specifically interacting with the regulator of G-protein signaling 9, and appears to function as the membrane anchor for the other largely soluble interacting partners. Mutations in this gene are associated with prolonged electroretinal response suppression (PERRS), also known as bradyopsia. [provided by RefSeq, Mar 2010]

RGS9BP links:

ANKRD27 (HGNC:25310): (ankyrin repeat domain 27) Enables guanyl-nucleotide exchange factor activity and small GTPase binding activity. Involved in endocytic recycling and negative regulation of SNARE complex assembly. Acts upstream of or within early endosome to late endosome transport. Located in endosome; lysosome; and plasma membrane. Implicated in eosinophilic esophagitis. [provided by Alliance of Genome Resources, Apr 2022]

ANKRD27 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP6

Variant 19-32676302-C-G is Benign according to our data. Variant chr19-32676302-C-G is described in ClinVar as [Benign]. Clinvar id is 498629.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=2.88 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RGS9BP	NM_207391.3 linkuse as main transcript	c.39C>G	p.Leu13Leu	synonymous_variant	1/1	ENST00000334176.4	NP_997274.2	Q6ZS82

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RGS9BP	ENST00000334176.4 linkuse as main transcript	c.39C>G	p.Leu13Leu	synonymous_variant	1/1	6	NM_207391.3	ENSP00000334134.3		Q6ZS82
ANKRD27	ENST00000590519.2 linkuse as main transcript	c.-547G>C		5_prime_UTR_variant	1/4	5		ENSP00000464819.1		K7EIN0

Frequencies

GnomAD3 genomes

AF:

0.0415

AC:

6312

AN:

152174

Hom.:

226

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0176

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.0461

Gnomad ASJ

AF:

0.0493

Gnomad EAS

AF:

0.210

Gnomad SAS

AF:

0.0628

Gnomad FIN

AF:

0.0526

Gnomad MID

AF:

0.0513

Gnomad NFE

AF:

0.0388

Gnomad OTH

AF:

0.0449

GnomAD3 exomes

AF:

0.0568

AC:

13723

AN:

241676

Hom.:

736

AF XY:

0.0560

AC XY:

7408

AN XY:

132330

show subpopulations

Gnomad AFR exome

AF:

0.0169

Gnomad AMR exome

AF:

0.0462

Gnomad ASJ exome

AF:

0.0521

Gnomad EAS exome

AF:

0.229

Gnomad SAS exome

AF:

0.0623

Gnomad FIN exome

AF:

0.0505

Gnomad NFE exome

AF:

0.0374

Gnomad OTH exome

AF:

0.0488

GnomAD4 exome

AF:

0.0433

AC:

63061

AN:

1455024

Hom.:

2227

Cov.:

AF XY:

0.0438

AC XY:

31655

AN XY:

723054

show subpopulations

Gnomad4 AFR exome

AF:

0.0143

Gnomad4 AMR exome

AF:

0.0458

Gnomad4 ASJ exome

AF:

0.0503

Gnomad4 EAS exome

AF:

0.230

Gnomad4 SAS exome

AF:

0.0597

Gnomad4 FIN exome

AF:

0.0521

Gnomad4 NFE exome

AF:

0.0357

Gnomad4 OTH exome

AF:

0.0418

GnomAD4 genome

AF:

0.0414

AC:

6307

AN:

152296

Hom.:

226

Cov.:

AF XY:

0.0439

AC XY:

3272

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.0175

Gnomad4 AMR

AF:

0.0461

Gnomad4 ASJ

AF:

0.0493

Gnomad4 EAS

AF:

0.210

Gnomad4 SAS

AF:

0.0632

Gnomad4 FIN

AF:

0.0526

Gnomad4 NFE

AF:

0.0388

Gnomad4 OTH

AF:

0.0445

Alfa

AF:

0.0416

Hom.:

Bravo

AF:

0.0402

Asia WGS

AF:

0.103

AC:

360

AN:

3476

EpiCase

AF:

0.0388

EpiControl

AF:

0.0400

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Eurofins Ntd Llc (ga)

Nov 17, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

DANN

Benign

0.63

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