rs10519914

chr4-147756460-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ARHGAP10	NM_024605.4	c.154+24005G>A		intron_variant		ENST00000336498.8
ARHGAP10	XM_005263215.4	c.154+24005G>A		intron_variant
ARHGAP10	XR_001741324.2	n.368+24005G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGAP10	ENST00000336498.8	c.154+24005G>A		intron_variant		1	NM_024605.4	P1
ARHGAP10	ENST00000510379.1	n.393+24005G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.0526

Gnomad4 ASJ AF: 0.0222

Gnomad4 EAS AF: 0.00520

Gnomad4 SAS AF: 0.0371

Gnomad4 FIN AF: 0.00179

Gnomad4 NFE AF: 0.00998

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0593 Hom.: 333

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

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

Other links and lift over

dbSNP: rs10519914; hg19: chr4-148677611;