rs10511389

chr3-119356010-T-G

Variant summary

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

The NM_020754.4(ARHGAP31):c.101-9306T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.071 in 152,186 control chromosomes in the GnomAD database, including 495 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 0.071 (495 hom., cov: 32)
• Consequence: ARHGAP31 NM_020754.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

ARHGAP31 (HGNC:29216): (Rho GTPase activating protein 31) This gene encodes a GTPase-activating protein (GAP). A variety of cellular processes are regulated by Rho GTPases which cycle between an inactive form bound to GDP and an active form bound to GTP. This cycling between inactive and active forms is regulated by guanine nucleotide exchange factors and GAPs. The encoded protein is a GAP shown to regulate two GTPases involved in protein trafficking and cell growth. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARHGAP31	NM_020754.4	c.101-9306T>G		intron_variant		ENST00000264245.9
ARHGAP31	XM_006713714.4	c.101-9306T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGAP31	ENST00000264245.9	c.101-9306T>G		intron_variant		1	NM_020754.4	P1
ARHGAP31	ENST00000482743.1	c.14-9306T>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0710 AC: 10803 AN: 152068 Hom.: 494 Cov.: 32

Gnomad AFR AF: 0.0278

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.0614

Gnomad ASJ AF: 0.0770

Gnomad EAS AF: 0.0861

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0989

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0904

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.0710 AC: 10807 AN: 152186 Hom.: 495 Cov.: 32 AF XY: 0.0728 AC XY: 5418 AN XY: 74392

Gnomad4 AFR AF: 0.0277

Gnomad4 AMR AF: 0.0613

Gnomad4 ASJ AF: 0.0770

Gnomad4 EAS AF: 0.0859

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0989

Gnomad4 NFE AF: 0.0904

Gnomad4 OTH AF: 0.0804

Alfa AF: 0.0860 Hom.: 342

Bravo AF: 0.0661

Asia WGS AF: 0.0950 AC: 329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.0
Dann	Benign	0.71

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: rs10511389; hg19: chr3-119074857;