11-128973957-G-T

Variant names:

• chr11-128973957-G-T
• rs3796668
• ENST00000524655.6:c.*135C>A

Variant summary

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

The ENST00000524655.6(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 ENST00000524655.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.627
• Publications: 2 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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000524655.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP32	NM_001378024.1	MANE Select	c.3073+167C>A		intron	N/A	NP_001364953.1	A0A804HK06
	ARHGAP32	NM_001142685.2		c.3031+167C>A		intron	N/A	NP_001136157.1	A7KAX9-1
	ARHGAP32	NM_001378025.1		c.2911+167C>A		intron	N/A	NP_001364954.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP32	ENST00000524655.6	TSL:1	c.*135C>A		3_prime_UTR	Exon 19 of 19	ENSP00000432468.2
	ARHGAP32	ENST00000682385.1	MANE Select	c.3073+167C>A		intron	N/A	ENSP00000507720.1	A0A804HK06
	ARHGAP32	ENST00000310343.13	TSL:1	c.3031+167C>A		intron	N/A	ENSP00000310561.8	A7KAX9-1

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

African (AFR) AF: 0.574 AC: 9030 AN: 15726

American (AMR) AF: 0.574 AC: 10400 AN: 18130

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 9022 AN: 14660

East Asian (EAS) AF: 0.601 AC: 19628 AN: 32638

South Asian (SAS) AF: 0.470 AC: 21615 AN: 45962

European-Finnish (FIN) AF: 0.622 AC: 19950 AN: 32054

Middle Eastern (MID) AF: 0.668 AC: 1532 AN: 2294

European-Non Finnish (NFE) AF: 0.658 AC: 274956 AN: 418114

Other (OTH) AF: 0.625 AC: 19755 AN: 31608

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

African (AFR) AF: 0.571 AC: 23633 AN: 41410

American (AMR) AF: 0.594 AC: 9070 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2227 AN: 3468

East Asian (EAS) AF: 0.585 AC: 3018 AN: 5160

South Asian (SAS) AF: 0.460 AC: 2202 AN: 4792

European-Finnish (FIN) AF: 0.622 AC: 6532 AN: 10510

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44399 AN: 67966

Other (OTH) AF: 0.604 AC: 1270 AN: 2102

Alfa AF: 0.637 Hom.: 11104

Bravo AF: 0.613

Asia WGS AF: 0.499 AC: 1734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.80
PhyloP100		0.63
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: rs3796668; hg19: chr11-128843852;