3-119364986-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_020754.4(ARHGAP31):c.101-330C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,794 control chromosomes in the GnomAD database, including 14,910 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.41 (14910 hom., cov: 31)
• Consequence: ARHGAP31 NM_020754.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.842

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BP6: Variant 3-119364986-C-T is Benign according to our data. Variant chr3-119364986-C-T is described in ClinVar as [Benign]. Clinvar id is 1255081.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARHGAP31	NM_020754.4	c.101-330C>T		intron_variant		ENST00000264245.9
ARHGAP31	XM_006713714.4	c.101-330C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGAP31	ENST00000264245.9	c.101-330C>T		intron_variant		1	NM_020754.4	P1
ARHGAP31	ENST00000482743.1	c.14-330C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62489 AN: 151676 Hom.: 14876 Cov.: 31

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.412 AC: 62587 AN: 151794 Hom.: 14910 Cov.: 31 AF XY: 0.410 AC XY: 30443 AN XY: 74174

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.393

Alfa AF: 0.364 Hom.: 1448

Bravo AF: 0.432

Asia WGS AF: 0.456 AC: 1583 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 16, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.4
Dann	Benign	0.52

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: rs6438524; hg19: chr3-119083833;