4-147756460-G-A

Variant names:

• chr4-147756460-G-A
• rs10519914
• NM_024605.4:c.154+24005G>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.154+24005G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,202 control chromosomes in the GnomAD database, including 3,444 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 0.12 (3444 hom., cov: 31)
• Consequence: ARHGAP10 NM_024605.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.985
• Publications: 1 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGAP10	NM_024605.4	c.154+24005G>A		intron_variant	Intron 1 of 22	ENST00000336498.8	NP_078881.3
ARHGAP10	XM_005263215.4	c.154+24005G>A		intron_variant	Intron 1 of 21		XP_005263272.1
ARHGAP10	XR_001741324.2	n.368+24005G>A		intron_variant	Intron 1 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP10	ENST00000336498.8	c.154+24005G>A		intron_variant	Intron 1 of 22	1	NM_024605.4	ENSP00000336923.3
ARHGAP10	ENST00000510379.1	n.393+24005G>A		intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18537 AN: 152086 Hom.: 3422 Cov.: 31

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0528

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.00558

Gnomad SAS AF: 0.0375

Gnomad FIN AF: 0.00179

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.00998

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.122 AC: 18596 AN: 152202 Hom.: 3444 Cov.: 31 AF XY: 0.118 AC XY: 8788 AN XY: 74438

African (AFR) AF: 0.399 AC: 16562 AN: 41484

American (AMR) AF: 0.0526 AC: 805 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0222 AC: 77 AN: 3464

East Asian (EAS) AF: 0.00520 AC: 27 AN: 5188

South Asian (SAS) AF: 0.0371 AC: 179 AN: 4826

European-Finnish (FIN) AF: 0.00179 AC: 19 AN: 10606

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.00998 AC: 679 AN: 68024

Other (OTH) AF: 0.107 AC: 226 AN: 2112

Alfa AF: 0.0569 Hom.: 514

Bravo AF: 0.139

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.076
DANN	Benign	0.39
PhyloP100		-0.98
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: rs10519914; hg19: chr4-148677611;