rs493172

Positions:

• chr11-129012984-G-C
• chr11-129012984-G-T

Variant summary

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

The NM_001378024.1(ARHGAP32):​c.1046-14516C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,188 control chromosomes in the GnomAD database, including 1,589 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 0.14 (1589 hom., cov: 32)
• Consequence: ARHGAP32 NM_001378024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARHGAP32	NM_001378024.1	c.1046-14516C>G		intron_variant		ENST00000682385.1	NP_001364953.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARHGAP32	ENST00000682385.1	c.1046-14516C>G		intron_variant			NM_001378024.1	ENSP00000507720.1

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21278 AN: 152070 Hom.: 1585 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.140 AC: 21287 AN: 152188 Hom.: 1589 Cov.: 32 AF XY: 0.140 AC XY: 10386 AN XY: 74408

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.127

Alfa AF: 0.0842 Hom.: 118

Bravo AF: 0.136

Asia WGS AF: 0.130 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.3
DANN	Benign	0.36

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: rs493172; hg19: chr11-128882879;