11-128965057-C-T

Variant summary

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

The 11-128965057-C-T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 151,924 control chromosomes in the GnomAD database, including 8,024 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 0.32 (8024 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ARHGAP32 NM_001378024.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARHGAP32	NM_001378024.1			downstream_gene_variant		ENST00000682385.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGAP32	ENST00000682385.1			downstream_gene_variant			NM_001378024.1	P3
ARHGAP32	ENST00000310343.13			downstream_gene_variant		1		A1

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48677 AN: 151806 Hom.: 8021 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.277

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.321 AC: 48693 AN: 151924 Hom.: 8024 Cov.: 32 AF XY: 0.322 AC XY: 23922 AN XY: 74230

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.275

Alfa AF: 0.335 Hom.: 11249

Bravo AF: 0.303

Asia WGS AF: 0.240 AC: 837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	13
Dann	Benign	0.51

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2298599; hg19: chr11-128834952;