rs10934491

Variant names:

• chr3-119349465-A-C
• rs10934491
• NM_020754.4:c.101-15851A>C

Your query was ambiguous. Multiple possible variants found:

• chr3-119349465-A-C
• chr3-119349465-A-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020754.4(ARHGAP31):​c.101-15851A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,048 control chromosomes in the GnomAD database, including 8,195 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 0.31 (8195 hom., cov: 32)
• Consequence: ARHGAP31 NM_020754.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 2 publications found

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 Gene-Disease associations (from GenCC):

• Adams-Oliver syndrome 1

  Inheritance: AD Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• Adams-Oliver syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020754.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP31	NM_020754.4	MANE Select	c.101-15851A>C		intron	N/A	NP_065805.2	A0A8S0MHV1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP31	ENST00000264245.9	TSL:1 MANE Select	c.101-15851A>C		intron	N/A	ENSP00000264245.4	Q2M1Z3
	ARHGAP31	ENST00000861944.1		c.101-15851A>C		intron	N/A	ENSP00000532003.1
	ARHGAP31	ENST00000482743.1	TSL:4	c.14-15851A>C		intron	N/A	ENSP00000418429.1	C9J652

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46314 AN: 151930 Hom.: 8180 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.305 AC: 46380 AN: 152048 Hom.: 8195 Cov.: 32 AF XY: 0.304 AC XY: 22611 AN XY: 74348

African (AFR) AF: 0.482 AC: 19979 AN: 41428

American (AMR) AF: 0.307 AC: 4690 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 610 AN: 3468

East Asian (EAS) AF: 0.287 AC: 1482 AN: 5166

South Asian (SAS) AF: 0.454 AC: 2186 AN: 4814

European-Finnish (FIN) AF: 0.187 AC: 1984 AN: 10596

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14486 AN: 67976

Other (OTH) AF: 0.298 AC: 629 AN: 2114

Alfa AF: 0.245 Hom.: 3055

Bravo AF: 0.322

Asia WGS AF: 0.409 AC: 1420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.0
DANN	Benign	0.68
PhyloP100		-0.063
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10934491; hg19: chr3-119068312;