chr4-147773019-C-T

Position:

• chr4-147773019-C-T

Variant summary

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

The NM_024605.4(ARHGAP10):​c.154+40564C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 152,156 control chromosomes in the GnomAD database, including 48,003 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 0.74 (48003 hom., cov: 32)
• Consequence: ARHGAP10 NM_024605.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARHGAP10	NM_024605.4	c.154+40564C>T		intron_variant		ENST00000336498.8	NP_078881.3
ARHGAP10	XM_005263215.4	c.154+40564C>T		intron_variant			XP_005263272.1
ARHGAP10	XR_001741324.2	n.368+40564C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARHGAP10	ENST00000336498.8	c.154+40564C>T		intron_variant		1	NM_024605.4	ENSP00000336923	P1
ARHGAP10	ENST00000510379.1	n.393+40564C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.744 AC: 113176 AN: 152038 Hom.: 48004 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.903

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.979

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.744 AC: 113185 AN: 152156 Hom.: 48003 Cov.: 32 AF XY: 0.750 AC XY: 55828 AN XY: 74392

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.903

Gnomad4 EAS AF: 0.872

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.979

Gnomad4 NFE AF: 0.929

Gnomad4 OTH AF: 0.774

Alfa AF: 0.819 Hom.: 9273

Bravo AF: 0.714

Asia WGS AF: 0.793 AC: 2758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.62

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: rs9332471; hg19: chr4-148694170;