rs13208724

Variant names:

• chr6-129695004-A-C
• rs13208724
• NM_033515.3:c.113+15020T>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033515.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP18	NM_033515.3	MANE Select	c.113+15020T>G		intron	N/A	NP_277050.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP18	ENST00000368149.3	TSL:1 MANE Select	c.113+15020T>G		intron	N/A	ENSP00000357131.2

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

African (AFR) AF: 0.157 AC: 6517 AN: 41530

American (AMR) AF: 0.220 AC: 3365 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 924 AN: 3470

East Asian (EAS) AF: 0.0647 AC: 336 AN: 5190

South Asian (SAS) AF: 0.337 AC: 1623 AN: 4822

European-Finnish (FIN) AF: 0.196 AC: 2076 AN: 10576

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18324 AN: 67982

Other (OTH) AF: 0.228 AC: 483 AN: 2114

Alfa AF: 0.249 Hom.: 2934

Bravo AF: 0.218

Asia WGS AF: 0.205 AC: 714 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.1
DANN	Benign	0.67
PhyloP100		0.50
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: rs13208724; hg19: chr6-130016149;