rs657820

chr11-129091800-C-Gchr11-129091800-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001378024.1(ARHGAP32):c.531+1821G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 151,782 control chromosomes in the GnomAD database, including 6,441 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 0.29 (6441 hom., cov: 32)
• Consequence: ARHGAP32 NM_001378024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARHGAP32	NM_001378024.1	c.531+1821G>C		intron_variant		ENST00000682385.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGAP32	ENST00000682385.1	c.531+1821G>C		intron_variant			NM_001378024.1	P3
ARHGAP32	ENST00000310343.13	c.489+1821G>C		intron_variant		1		A1
ARHGAP32	ENST00000524655.5	c.267+1821G>C		intron_variant		1
ARHGAP32	ENST00000525234.1	c.411+1821G>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43778 AN: 151664 Hom.: 6436 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.289 AC: 43810 AN: 151782 Hom.: 6441 Cov.: 32 AF XY: 0.288 AC XY: 21355 AN XY: 74184

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.288

Alfa AF: 0.276 Hom.: 803

Bravo AF: 0.295

Asia WGS AF: 0.275 AC: 959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	7.4
Dann	Benign	0.68

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: rs657820; hg19: chr11-128961695;