NM_001378024.1:c.531+1821G>C

Variant names:

• chr11-129091800-C-G
• rs657820
• NM_001378024.1:c.531+1821G>C

Variant summary

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

The NM_001378024.1(ARHGAP32):​c.531+1821G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 151,782 control chromosomes in the GnomAD database, including 6,441 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 0.29 (6441 hom., cov: 32)
• Consequence: ARHGAP32 NM_001378024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 0 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001378024.1. 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.531+1821G>C		intron	N/A	NP_001364953.1	A0A804HK06
	ARHGAP32	NM_001142685.2		c.489+1821G>C		intron	N/A	NP_001136157.1	A7KAX9-1
	ARHGAP32	NM_001378025.1		c.369+1821G>C		intron	N/A	NP_001364954.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP32	ENST00000682385.1	MANE Select	c.531+1821G>C		intron	N/A	ENSP00000507720.1	A0A804HK06
	ARHGAP32	ENST00000310343.13	TSL:1	c.489+1821G>C		intron	N/A	ENSP00000310561.8	A7KAX9-1
	ARHGAP32	ENST00000524655.6	TSL:1	c.291+1821G>C		intron	N/A	ENSP00000432468.2

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43778 AN: 151664 Hom.: 6436 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.289 AC: 43810 AN: 151782 Hom.: 6441 Cov.: 32 AF XY: 0.288 AC XY: 21355 AN XY: 74184

African (AFR) AF: 0.346 AC: 14316 AN: 41410

American (AMR) AF: 0.298 AC: 4544 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 751 AN: 3464

East Asian (EAS) AF: 0.275 AC: 1424 AN: 5172

South Asian (SAS) AF: 0.265 AC: 1278 AN: 4816

European-Finnish (FIN) AF: 0.266 AC: 2807 AN: 10558

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.261 AC: 17702 AN: 67816

Other (OTH) AF: 0.288 AC: 605 AN: 2102

Alfa AF: 0.276 Hom.: 803

Bravo AF: 0.295

Asia WGS AF: 0.275 AC: 959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.4
DANN	Benign	0.68
PhyloP100		1.3
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: rs657820; hg19: chr11-128961695;