3-119295140-CT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_020754.4(ARHGAP31):c.100+148del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 542,454 control chromosomes in the GnomAD database, including 10,512 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.28 (7082 hom., cov: 17)
  • Exomes 𝑓: 0.31 (3430 hom.)
• Consequence: ARHGAP31 NM_020754.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0770

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 -10 ACMG points.

• BP6: Variant 3-119295140-CT-C is Benign according to our data. Variant chr3-119295140-CT-C is described in ClinVar as [Benign]. Clinvar id is 1290204.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARHGAP31	NM_020754.4	c.100+148del		intron_variant		ENST00000264245.9
ARHGAP31	XM_006713714.4	c.100+148del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGAP31	ENST00000264245.9	c.100+148del		intron_variant		1	NM_020754.4	P1

Frequencies

GnomAD3 genomes AF: 0.283 AC: 39523 AN: 139438 Hom.: 7060 Cov.: 17

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.0731

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.183

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.253

GnomAD4 exome AF: 0.306 AC: 123471 AN: 402948 Hom.: 3430 AF XY: 0.311 AC XY: 66952 AN XY: 215368

Gnomad4 AFR exome AF: 0.503

Gnomad4 AMR exome AF: 0.309

Gnomad4 ASJ exome AF: 0.312

Gnomad4 EAS exome AF: 0.292

Gnomad4 SAS exome AF: 0.384

Gnomad4 FIN exome AF: 0.307

Gnomad4 NFE exome AF: 0.285

Gnomad4 OTH exome AF: 0.331

GnomAD4 genome AF: 0.284 AC: 39599 AN: 139506 Hom.: 7082 Cov.: 17 AF XY: 0.284 AC XY: 19130 AN XY: 67398

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.260

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

Aug 08, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10707359; hg19: chr3-119013987;