11-128973957-G-T

Variant summary

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

The ENST00000524655.5(ARHGAP32):c.*135C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 763,066 control chromosomes in the GnomAD database, including 152,138 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 0.61 (28802 hom., cov: 31)
  • Exomes 𝑓: 0.63 (123336 hom.)
• Consequence: ARHGAP32 ENST00000524655.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.627

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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARHGAP32	NM_001378024.1	c.3073+167C>A		intron_variant		ENST00000682385.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGAP32	ENST00000682385.1	c.3073+167C>A		intron_variant			NM_001378024.1	P3

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93135 AN: 151762 Hom.: 28794 Cov.: 31

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.606

GnomAD4 exome AF: 0.631 AC: 385888 AN: 611186 Hom.: 123336 Cov.: 8 AF XY: 0.625 AC XY: 196884 AN XY: 314776

Gnomad4 AFR exome AF: 0.574

Gnomad4 AMR exome AF: 0.574

Gnomad4 ASJ exome AF: 0.615

Gnomad4 EAS exome AF: 0.601

Gnomad4 SAS exome AF: 0.470

Gnomad4 FIN exome AF: 0.622

Gnomad4 NFE exome AF: 0.658

Gnomad4 OTH exome AF: 0.625

GnomAD4 genome AF: 0.614 AC: 93181 AN: 151880 Hom.: 28802 Cov.: 31 AF XY: 0.611 AC XY: 45314 AN XY: 74206

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.604

Alfa AF: 0.632 Hom.: 6740

Bravo AF: 0.613

Asia WGS AF: 0.499 AC: 1734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	12
Dann	Benign	0.80

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: rs3796668; hg19: chr11-128843852;