3-119388405-T-G

Position:

• chr3-119388405-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.683-2380T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.814 in 151,048 control chromosomes in the GnomAD database, including 50,254 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 0.81 (50254 hom., cov: 28)
• Consequence: ARHGAP31 NM_020754.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARHGAP31	NM_020754.4	c.683-2380T>G		intron_variant		ENST00000264245.9	NP_065805.2
ARHGAP31	XM_006713714.4	c.683-2380T>G		intron_variant			XP_006713777.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARHGAP31	ENST00000264245.9	c.683-2380T>G		intron_variant		1	NM_020754.4	ENSP00000264245.4

Frequencies

GnomAD3 genomes AF: 0.814 AC: 122797 AN: 150938 Hom.: 50209 Cov.: 28

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.790

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.814 AC: 122894 AN: 151048 Hom.: 50254 Cov.: 28 AF XY: 0.811 AC XY: 59826 AN XY: 73780

Gnomad4 AFR AF: 0.901

Gnomad4 AMR AF: 0.739

Gnomad4 ASJ AF: 0.762

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.858

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.779

Gnomad4 OTH AF: 0.806

Alfa AF: 0.790 Hom.: 26867

Bravo AF: 0.815

Asia WGS AF: 0.878 AC: 3052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.72

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: rs6766899; hg19: chr3-119107252;