chr4-147754042-T-C

Variant names:

• chr4-147754042-T-C
• rs13124167
• NM_024605.4:c.154+21587T>C

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+21587T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0741 in 152,262 control chromosomes in the GnomAD database, including 523 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 0.074 (523 hom., cov: 32)
• Consequence: ARHGAP10 NM_024605.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• 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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGAP10	NM_024605.4	c.154+21587T>C		intron_variant	Intron 1 of 22	ENST00000336498.8	NP_078881.3
ARHGAP10	XM_005263215.4	c.154+21587T>C		intron_variant	Intron 1 of 21		XP_005263272.1
ARHGAP10	XR_001741324.2	n.368+21587T>C		intron_variant	Intron 1 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP10	ENST00000336498.8	c.154+21587T>C		intron_variant	Intron 1 of 22	1	NM_024605.4	ENSP00000336923.3
ARHGAP10	ENST00000510379.1	n.393+21587T>C		intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes AF: 0.0741 AC: 11279 AN: 152144 Hom.: 523 Cov.: 32

Gnomad AFR AF: 0.0199

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0631

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0447

Gnomad FIN AF: 0.0892

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0844

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

GnomAD4 genome AF: 0.0741 AC: 11276 AN: 152262 Hom.: 523 Cov.: 32 AF XY: 0.0713 AC XY: 5311 AN XY: 74444

African (AFR) AF: 0.0198 AC: 825 AN: 41568

American (AMR) AF: 0.0629 AC: 962 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 402 AN: 3472

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5184

South Asian (SAS) AF: 0.0449 AC: 217 AN: 4832

European-Finnish (FIN) AF: 0.0892 AC: 945 AN: 10596

Middle Eastern (MID) AF: 0.0582 AC: 17 AN: 292

European-Non Finnish (NFE) AF: 0.113 AC: 7656 AN: 68008

Other (OTH) AF: 0.0835 AC: 176 AN: 2108

Alfa AF: 0.0876 Hom.: 558

Bravo AF: 0.0712

Asia WGS AF: 0.0280 AC: 97 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.3
DANN	Benign	0.79
PhyloP100		0.043
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: rs13124167; hg19: chr4-148675193;