rs4662198

Variant names:

• chr2-143290158-G-T
• rs4662198
• NM_018460.4:c.474+39558G>T

Variant summary

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

The NM_018460.4(ARHGAP15):​c.474+39558G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,014 control chromosomes in the GnomAD database, including 4,167 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 0.22 (4167 hom., cov: 31)
• Consequence: ARHGAP15 NM_018460.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 7 publications found

Genes affected

ARHGAP15 (HGNC:21030): (Rho GTPase activating protein 15) RHO GTPases (see ARHA; MIM 165390) regulate diverse biologic processes, and their activity is regulated by RHO GTPase-activating proteins (GAPs), such as ARHGAP15 (Seoh et al., 2003 [PubMed 12650940]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018460.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP15	NM_018460.4	MANE Select	c.474+39558G>T		intron	N/A	NP_060930.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP15	ENST00000295095.11	TSL:1 MANE Select	c.474+39558G>T		intron	N/A	ENSP00000295095.6	Q53QZ3
	ARHGAP15	ENST00000906468.1		c.474+39558G>T		intron	N/A	ENSP00000576527.1
	ARHGAP15	ENST00000906471.1		c.474+39558G>T		intron	N/A	ENSP00000576530.1

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33316 AN: 151894 Hom.: 4164 Cov.: 31

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.219 AC: 33340 AN: 152014 Hom.: 4167 Cov.: 31 AF XY: 0.226 AC XY: 16777 AN XY: 74290

African (AFR) AF: 0.135 AC: 5593 AN: 41464

American (AMR) AF: 0.387 AC: 5899 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 778 AN: 3470

East Asian (EAS) AF: 0.343 AC: 1766 AN: 5152

South Asian (SAS) AF: 0.390 AC: 1883 AN: 4828

European-Finnish (FIN) AF: 0.196 AC: 2071 AN: 10576

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14460 AN: 67964

Other (OTH) AF: 0.244 AC: 515 AN: 2112

Alfa AF: 0.230 Hom.: 7425

Bravo AF: 0.231

Asia WGS AF: 0.352 AC: 1220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.54
PhyloP100		0.072
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: rs4662198; hg19: chr2-144047727;