rs13208724

Positions:

• chr6-129695004-A-C
• chr6-129695004-A-T

Variant summary

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

The NM_033515.3(ARHGAP18):​c.113+15020T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,176 control chromosomes in the GnomAD database, including 4,126 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 (4126 hom., cov: 33)
• Consequence: ARHGAP18 NM_033515.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502

Genes affected

ARHGAP18 (HGNC:21035): (Rho GTPase activating protein 18) Enables GTPase activator activity. Involved in several processes, including regulation of actin filament polymerization; regulation of small GTPase mediated signal transduction; and small GTPase mediated signal transduction. Located in cytosol; nuclear speck; and plasma membrane. Part of cytoplasmic microtubule and ruffle. Implicated in schizophrenia. [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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARHGAP18	NM_033515.3	c.113+15020T>G		intron_variant		ENST00000368149.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGAP18	ENST00000368149.3	c.113+15020T>G		intron_variant		1	NM_033515.3	P1

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33852 AN: 152058 Hom.: 4119 Cov.: 33

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.0644

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.223 AC: 33868 AN: 152176 Hom.: 4126 Cov.: 33 AF XY: 0.219 AC XY: 16276 AN XY: 74404

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.0647

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.228

Alfa AF: 0.248 Hom.: 2633

Bravo AF: 0.218

Asia WGS AF: 0.205 AC: 714 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.1
DANN	Benign	0.67

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: rs13208724; hg19: chr6-130016149;