NM_024605.4:c.154+42350G>T

Variant names:

• chr4-147774805-G-T
• rs964170
• NM_024605.4:c.154+42350G>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.154+42350G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 152,114 control chromosomes in the GnomAD database, including 48,710 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 (48710 hom., cov: 31)
• Consequence: ARHGAP10 NM_024605.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 6 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGAP10	NM_024605.4	c.154+42350G>T		intron_variant	Intron 1 of 22	ENST00000336498.8	NP_078881.3
ARHGAP10	XM_005263215.4	c.154+42350G>T		intron_variant	Intron 1 of 21		XP_005263272.1
ARHGAP10	XR_001741324.2	n.368+42350G>T		intron_variant	Intron 1 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP10	ENST00000336498.8	c.154+42350G>T		intron_variant	Intron 1 of 22	1	NM_024605.4	ENSP00000336923.3
ARHGAP10	ENST00000510379.1	n.393+42350G>T		intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes AF: 0.750 AC: 113965 AN: 151996 Hom.: 48710 Cov.: 31

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.938

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.749 AC: 113975 AN: 152114 Hom.: 48710 Cov.: 31 AF XY: 0.755 AC XY: 56187 AN XY: 74372

African (AFR) AF: 0.300 AC: 12419 AN: 41420

American (AMR) AF: 0.856 AC: 13066 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3155 AN: 3472

East Asian (EAS) AF: 0.871 AC: 4507 AN: 5172

South Asian (SAS) AF: 0.826 AC: 3990 AN: 4828

European-Finnish (FIN) AF: 0.983 AC: 10437 AN: 10620

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.938 AC: 63762 AN: 68012

Other (OTH) AF: 0.779 AC: 1646 AN: 2112

Alfa AF: 0.893 Hom.: 96977

Bravo AF: 0.719

Asia WGS AF: 0.798 AC: 2777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.6
DANN	Benign	0.74
PhyloP100		0.039
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: rs964170; hg19: chr4-148695956;