4-147766488-T-C

Position:

• chr4-147766488-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024605.4(ARHGAP10):​c.154+34033T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 151,356 control chromosomes in the GnomAD database, including 48,053 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 (48053 hom., cov: 27)
• Consequence: ARHGAP10 NM_024605.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660

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]

ARHGAP10 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARHGAP10	NM_024605.4	c.154+34033T>C		intron_variant		ENST00000336498.8	NP_078881.3
ARHGAP10	XM_005263215.4	c.154+34033T>C		intron_variant			XP_005263272.1
ARHGAP10	XR_001741324.2	n.368+34033T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARHGAP10	ENST00000336498.8	c.154+34033T>C		intron_variant		1	NM_024605.4	ENSP00000336923.3
ARHGAP10	ENST00000510379.1	n.393+34033T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.747 AC: 112928 AN: 151238 Hom.: 48057 Cov.: 27

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.979

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.746 AC: 112931 AN: 151356 Hom.: 48053 Cov.: 27 AF XY: 0.752 AC XY: 55631 AN XY: 73944

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.857

Gnomad4 ASJ AF: 0.907

Gnomad4 EAS AF: 0.903

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.979

Gnomad4 NFE AF: 0.931

Gnomad4 OTH AF: 0.777

Alfa AF: 0.821 Hom.: 9027

Bravo AF: 0.717

Asia WGS AF: 0.807 AC: 2807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.48

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: rs6822971; hg19: chr4-148687639;