3-119399949-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.1069+688T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,062 control chromosomes in the GnomAD database, including 8,573 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 0.30 (8573 hom., cov: 32)
• Consequence: ARHGAP31 NM_020754.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.788

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]

LOC124906273 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARHGAP31	NM_020754.4	c.1069+688T>G		intron_variant		ENST00000264245.9
LOC124906273	XR_007096027.1	n.7810A>C		non_coding_transcript_exon_variant	2/2
ARHGAP31	XM_006713714.4	c.1069+688T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGAP31	ENST00000264245.9	c.1069+688T>G		intron_variant		1	NM_020754.4	P1

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46130 AN: 151942 Hom.: 8568 Cov.: 32

Gnomad AFR AF: 0.0781

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.303 AC: 46146 AN: 152062 Hom.: 8573 Cov.: 32 AF XY: 0.308 AC XY: 22875 AN XY: 74330

Gnomad4 AFR AF: 0.0780

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.314

Alfa AF: 0.377 Hom.: 21772

Bravo AF: 0.294

Asia WGS AF: 0.318 AC: 1106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	5.7
Dann	Benign	0.80

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: rs11712165; hg19: chr3-119118796;