rs10519921

Variant names:

• chr4-147916191-C-T
• rs10519921
• NM_024605.4:c.1228+3052C>T

Variant summary

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

The NM_024605.4(ARHGAP10):​c.1228+3052C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,132 control chromosomes in the GnomAD database, including 2,981 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 0.13 (2981 hom., cov: 32)
• Consequence: ARHGAP10 NM_024605.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253
• Publications: 0 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGAP10	NM_024605.4	c.1228+3052C>T		intron_variant	Intron 13 of 22	ENST00000336498.8	NP_078881.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP10	ENST00000336498.8	c.1228+3052C>T		intron_variant	Intron 13 of 22	1	NM_024605.4	ENSP00000336923.3
ARHGAP10	ENST00000506054.5	n.6360+3052C>T		intron_variant	Intron 7 of 16	1
ARHGAP10	ENST00000507661.1	c.259+3052C>T		intron_variant	Intron 4 of 12	2		ENSP00000422358.1

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19546 AN: 152014 Hom.: 2961 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0352

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.0778

Gnomad FIN AF: 0.0179

Gnomad MID AF: 0.0897

Gnomad NFE AF: 0.0123

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.129 AC: 19614 AN: 152132 Hom.: 2981 Cov.: 32 AF XY: 0.127 AC XY: 9450 AN XY: 74384

African (AFR) AF: 0.360 AC: 14907 AN: 41440

American (AMR) AF: 0.131 AC: 2003 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0352 AC: 122 AN: 3468

East Asian (EAS) AF: 0.178 AC: 919 AN: 5174

South Asian (SAS) AF: 0.0773 AC: 373 AN: 4826

European-Finnish (FIN) AF: 0.0179 AC: 190 AN: 10614

Middle Eastern (MID) AF: 0.0931 AC: 27 AN: 290

European-Non Finnish (NFE) AF: 0.0123 AC: 835 AN: 68014

Other (OTH) AF: 0.112 AC: 237 AN: 2114

Alfa AF: 0.0780 Hom.: 215

Bravo AF: 0.152

Asia WGS AF: 0.160 AC: 555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.78
DANN	Benign	0.55
PhyloP100		-0.25
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: rs10519921; hg19: chr4-148837342;