rs187006

Variant names:

• chr4-147945437-T-A
• rs187006
• NM_024605.4:c.1304-1180T>A

Variant summary

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

The NM_024605.4(ARHGAP10):​c.1304-1180T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 152,110 control chromosomes in the GnomAD database, including 47,022 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 0.75 (47022 hom., cov: 32)
• Consequence: ARHGAP10 NM_024605.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.716
• Publications: 2 publications found

Genes affected

ARHGAP10 (HGNC:26099): (Rho GTPase activating protein 10) Predicted to enable GTPase activator activity. Predicted to be involved in cytoskeleton organization and negative regulation of apoptotic process. Predicted to be located in perinuclear region of cytoplasm and plasma membrane. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGAP10	NM_024605.4	c.1304-1180T>A		intron_variant	Intron 14 of 22	ENST00000336498.8	NP_078881.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP10	ENST00000336498.8	c.1304-1180T>A		intron_variant	Intron 14 of 22	1	NM_024605.4	ENSP00000336923.3
ARHGAP10	ENST00000506054.5	n.6436-1180T>A		intron_variant	Intron 8 of 16	1
ARHGAP10	ENST00000507661.1	c.335-1180T>A		intron_variant	Intron 5 of 12	2		ENSP00000422358.1

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114326 AN: 151992 Hom.: 47027 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.883

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.793

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

GnomAD4 genome AF: 0.752 AC: 114345 AN: 152110 Hom.: 47022 Cov.: 32 AF XY: 0.755 AC XY: 56166 AN XY: 74346

African (AFR) AF: 0.390 AC: 16159 AN: 41426

American (AMR) AF: 0.794 AC: 12142 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.883 AC: 3065 AN: 3470

East Asian (EAS) AF: 0.673 AC: 3482 AN: 5174

South Asian (SAS) AF: 0.846 AC: 4077 AN: 4818

European-Finnish (FIN) AF: 0.908 AC: 9612 AN: 10588

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.926 AC: 63010 AN: 68024

Other (OTH) AF: 0.791 AC: 1673 AN: 2114

Alfa AF: 0.832 Hom.: 6898

Bravo AF: 0.723

Asia WGS AF: 0.721 AC: 2509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.52
DANN	Benign	0.71
PhyloP100		-0.72
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: rs187006; hg19: chr4-148866588;