6-129615686-C-T

Variant names:

• chr6-129615686-C-T
• rs9388717
• NM_033515.3:c.1044+526G>A

Variant summary

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

The NM_033515.3(ARHGAP18):​c.1044+526G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,990 control chromosomes in the GnomAD database, including 14,781 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 0.44 (14781 hom., cov: 32)
• Consequence: ARHGAP18 NM_033515.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681
• Publications: 4 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.471 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP18	NM_033515.3	MANE Select	c.1044+526G>A		intron	N/A	NP_277050.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP18	ENST00000368149.3	TSL:1 MANE Select	c.1044+526G>A		intron	N/A	ENSP00000357131.2
	ARHGAP18	ENST00000909755.1		c.957+526G>A		intron	N/A	ENSP00000579814.1
	ARHGAP18	ENST00000938085.1		c.787-7634G>A		intron	N/A	ENSP00000608144.1

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66201 AN: 151872 Hom.: 14760 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.436 AC: 66265 AN: 151990 Hom.: 14781 Cov.: 32 AF XY: 0.434 AC XY: 32265 AN XY: 74282

African (AFR) AF: 0.477 AC: 19746 AN: 41404

American (AMR) AF: 0.425 AC: 6488 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1346 AN: 3470

East Asian (EAS) AF: 0.292 AC: 1512 AN: 5174

South Asian (SAS) AF: 0.287 AC: 1386 AN: 4822

European-Finnish (FIN) AF: 0.470 AC: 4958 AN: 10556

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29447 AN: 67972

Other (OTH) AF: 0.457 AC: 965 AN: 2110

Alfa AF: 0.423 Hom.: 10648

Bravo AF: 0.437

Asia WGS AF: 0.326 AC: 1133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	13
DANN	Benign	0.62
PhyloP100		-0.68
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: rs9388717; hg19: chr6-129936831;