rs546239

Variant names:

• chr11-128965863-C-T
• rs546239
• NM_001378024.1:c.*3044G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000682385.1(ARHGAP32):​c.*3044G>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 0.885 in 152,228 control chromosomes in the GnomAD database, including 59,743 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 0.88 (59742 hom., cov: 31)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: ARHGAP32 ENST00000682385.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.381
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000682385.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP32	NM_001378024.1	MANE Select	c.*3044G>A		3_prime_UTR	Exon 23 of 23	NP_001364953.1
	ARHGAP32	NM_001142685.2		c.*3044G>A		3_prime_UTR	Exon 22 of 22	NP_001136157.1
	ARHGAP32	NM_001378025.1		c.*3044G>A		3_prime_UTR	Exon 22 of 22	NP_001364954.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP32	ENST00000682385.1	MANE Select	c.*3044G>A		3_prime_UTR	Exon 23 of 23	ENSP00000507720.1
	ARHGAP32	ENST00000310343.13	TSL:1	c.*3044G>A		3_prime_UTR	Exon 22 of 22	ENSP00000310561.8

Frequencies

GnomAD3 genomes AF: 0.885 AC: 134556 AN: 152108 Hom.: 59703 Cov.: 31

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.880

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.885 AC: 134650 AN: 152226 Hom.: 59742 Cov.: 31 AF XY: 0.882 AC XY: 65606 AN XY: 74420

African (AFR) AF: 0.940 AC: 39043 AN: 41552

American (AMR) AF: 0.858 AC: 13119 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 2840 AN: 3470

East Asian (EAS) AF: 0.809 AC: 4180 AN: 5164

South Asian (SAS) AF: 0.683 AC: 3293 AN: 4820

European-Finnish (FIN) AF: 0.895 AC: 9491 AN: 10602

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.878 AC: 59732 AN: 68006

Other (OTH) AF: 0.876 AC: 1853 AN: 2116

Alfa AF: 0.877 Hom.: 25083

Bravo AF: 0.890

Asia WGS AF: 0.731 AC: 2546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.38
DANN	Benign	0.71
PhyloP100		-0.38
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs546239; hg19: chr11-128835758;