Variant chr11-128969261-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001378024.1(ARHGAP32):c.5952A>G(p.Glu1984=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0747 in 1,614,106 control chromosomes in the GnomAD database, including 4,837 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.081 ( 563 hom., cov: 32)

Exomes 𝑓: 0.074 ( 4274 hom. )

Consequence

ARHGAP32
NM_001378024.1 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.43

Variant links:

Genes affected

ARHGAP32 (HGNC:17399): (Rho GTPase activating protein 32) RICS is a neuron-associated GTPase-activating protein that may regulate dendritic spine morphology and strength by modulating Rho GTPase (see RHOA; MIM 165390) activity (Okabe et al., 2003 [PubMed 12531901]).[supplied by OMIM, Mar 2008]

ARHGAP32 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 11-128969261-T-C is Benign according to our data. Variant chr11-128969261-T-C is described in ClinVar as [Benign]. Clinvar id is 3055563.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-1.43 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARHGAP32	NM_001378024.1 linkuse as main transcript	c.5952A>G	p.Glu1984=	synonymous_variant	23/23	ENST00000682385.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGAP32	ENST00000682385.1 linkuse as main transcript	c.5952A>G	p.Glu1984=	synonymous_variant	23/23		NM_001378024.1	P3

Frequencies

GnomAD3 genomes

AF:

0.0813

AC:

12376

AN:

152184

Hom.:

563

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0920

Gnomad AMI

AF:

0.142

Gnomad AMR

AF:

0.0608

Gnomad ASJ

AF:

0.0602

Gnomad EAS

AF:

0.0541

Gnomad SAS

AF:

0.0275

Gnomad FIN

AF:

0.125

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0790

Gnomad OTH

AF:

0.0746

GnomAD3 exomes

AF:

0.0703

AC:

17665

AN:

251366

Hom.:

723

AF XY:

0.0691

AC XY:

9381

AN XY:

135852

show subpopulations

Gnomad AFR exome

AF:

0.0924

Gnomad AMR exome

AF:

0.0432

Gnomad ASJ exome

AF:

0.0647

Gnomad EAS exome

AF:

0.0525

Gnomad SAS exome

AF:

0.0299

Gnomad FIN exome

AF:

0.122

Gnomad NFE exome

AF:

0.0792

Gnomad OTH exome

AF:

0.0794

GnomAD4 exome

AF:

0.0740

AC:

108214

AN:

1461804

Hom.:

4274

Cov.:

AF XY:

0.0728

AC XY:

52977

AN XY:

727208

show subpopulations

Gnomad4 AFR exome

AF:

0.0929

Gnomad4 AMR exome

AF:

0.0459

Gnomad4 ASJ exome

AF:

0.0643

Gnomad4 EAS exome

AF:

0.0564

Gnomad4 SAS exome

AF:

0.0285

Gnomad4 FIN exome

AF:

0.126

Gnomad4 NFE exome

AF:

0.0764

Gnomad4 OTH exome

AF:

0.0777

GnomAD4 genome

AF:

0.0813

AC:

12386

AN:

152302

Hom.:

563

Cov.:

AF XY:

0.0819

AC XY:

6103

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.0921

Gnomad4 AMR

AF:

0.0607

Gnomad4 ASJ

AF:

0.0602

Gnomad4 EAS

AF:

0.0544

Gnomad4 SAS

AF:

0.0269

Gnomad4 FIN

AF:

0.125

Gnomad4 NFE

AF:

0.0790

Gnomad4 OTH

AF:

0.0738

Alfa

AF:

0.0778

Hom.:

751

Bravo

AF:

0.0779

Asia WGS

AF:

0.0460

AC:

163

AN:

3478

EpiCase

AF:

0.0773

EpiControl

AF:

0.0840

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ARHGAP32-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 17, 2020

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.1

DANN

Benign

0.51

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