Variant 3-119295081-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_020754.4(ARHGAP31):c.100+77A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 1,375,806 control chromosomes in the GnomAD database, including 153,843 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.47 ( 16301 hom., cov: 25)

Exomes 𝑓: 0.47 ( 137542 hom. )

Consequence

ARHGAP31
NM_020754.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.846

Variant links:

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]

ARHGAP31 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 3-119295081-A-T is Benign according to our data. Variant chr3-119295081-A-T is described in ClinVar as [Benign]. Clinvar id is 1277783.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARHGAP31	NM_020754.4 linkuse as main transcript	c.100+77A>T		intron_variant		ENST00000264245.9	NP_065805.2	Q2M1Z3A0A8S0MHV1
ARHGAP31	XM_006713714.4 linkuse as main transcript	c.100+77A>T		intron_variant			XP_006713777.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARHGAP31	ENST00000264245.9 linkuse as main transcript	c.100+77A>T		intron_variant		1	NM_020754.4	ENSP00000264245.4		Q2M1Z3

Frequencies

GnomAD3 genomes

AF:

0.472

AC:

69627

AN:

147592

Hom.:

16300

Cov.:

show subpopulations

Gnomad AFR

AF:

0.465

Gnomad AMI

AF:

0.391

Gnomad AMR

AF:

0.495

Gnomad ASJ

AF:

0.448

Gnomad EAS

AF:

0.451

Gnomad SAS

AF:

0.467

Gnomad FIN

AF:

0.511

Gnomad MID

AF:

0.446

Gnomad NFE

AF:

0.470

Gnomad OTH

AF:

0.466

GnomAD4 exome

AF:

0.472

AC:

579560

AN:

1228152

Hom.:

137542

AF XY:

0.471

AC XY:

293102

AN XY:

621682

show subpopulations

Gnomad4 AFR exome

AF:

0.453

Gnomad4 AMR exome

AF:

0.544

Gnomad4 ASJ exome

AF:

0.476

Gnomad4 EAS exome

AF:

0.466

Gnomad4 SAS exome

AF:

0.474

Gnomad4 FIN exome

AF:

0.507

Gnomad4 NFE exome

AF:

0.468

Gnomad4 OTH exome

AF:

0.457

GnomAD4 genome

AF:

0.472

AC:

69654

AN:

147654

Hom.:

16301

Cov.:

AF XY:

0.473

AC XY:

33926

AN XY:

71700

show subpopulations

Gnomad4 AFR

AF:

0.465

Gnomad4 AMR

AF:

0.495

Gnomad4 ASJ

AF:

0.448

Gnomad4 EAS

AF:

0.451

Gnomad4 SAS

AF:

0.468

Gnomad4 FIN

AF:

0.511

Gnomad4 NFE

AF:

0.470

Gnomad4 OTH

AF:

0.463

Alfa

AF:

0.473

Hom.:

2085

Bravo

AF:

0.466

Asia WGS

AF:

0.448

AC:

1562

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 16, 2018	- -

Adams-Oliver syndrome 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Dec 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

5.5

DANN

Benign

0.60

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over