rs6935162

chr6-129586442-G-T

Variant summary

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

The NM_033515.3(ARHGAP18):c.1714-2330C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,690 control chromosomes in the GnomAD database, including 5,928 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 0.28 (5928 hom., cov: 31)
• Consequence: ARHGAP18 NM_033515.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.896

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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARHGAP18	NM_033515.3	c.1714-2330C>A		intron_variant		ENST00000368149.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGAP18	ENST00000368149.3	c.1714-2330C>A		intron_variant		1	NM_033515.3	P1
ARHGAP18	ENST00000463225.1	n.92-2330C>A		intron_variant, non_coding_transcript_variant		3
ARHGAP18	ENST00000483367.5	n.88-2330C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41727 AN: 151572 Hom.: 5932 Cov.: 31

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.275 AC: 41717 AN: 151690 Hom.: 5928 Cov.: 31 AF XY: 0.275 AC XY: 20378 AN XY: 74106

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.277

Alfa AF: 0.306 Hom.: 15412

Bravo AF: 0.267

Asia WGS AF: 0.318 AC: 1111 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.5
Dann	Benign	0.25

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: rs6935162; hg19: chr6-129907587; COSMIC: COSV63765939;