rs6922711

Variant names:

• chr6-129665647-T-C
• rs6922711
• NM_033515.3:c.114-23629A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-129665647-T-C
• chr6-129665647-T-G

Variant summary

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

The NM_033515.3(ARHGAP18):​c.114-23629A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 152,076 control chromosomes in the GnomAD database, including 21,469 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 0.52 (21469 hom., cov: 32)
• Consequence: ARHGAP18 NM_033515.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 3 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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.67 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.114-23629A>G		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.114-23629A>G		intron	N/A	ENSP00000357131.2	Q8N392-1
	ARHGAP18	ENST00000909755.1		c.114-23629A>G		intron	N/A	ENSP00000579814.1
	ARHGAP18	ENST00000938085.1		c.114-23629A>G		intron	N/A	ENSP00000608144.1

Frequencies

GnomAD3 genomes AF: 0.520 AC: 79053 AN: 151954 Hom.: 21415 Cov.: 32

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.521 AC: 79169 AN: 152076 Hom.: 21469 Cov.: 32 AF XY: 0.521 AC XY: 38690 AN XY: 74306

African (AFR) AF: 0.676 AC: 28067 AN: 41502

American (AMR) AF: 0.469 AC: 7173 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1689 AN: 3468

East Asian (EAS) AF: 0.414 AC: 2140 AN: 5172

South Asian (SAS) AF: 0.477 AC: 2297 AN: 4816

European-Finnish (FIN) AF: 0.503 AC: 5308 AN: 10544

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30917 AN: 67974

Other (OTH) AF: 0.533 AC: 1127 AN: 2114

Alfa AF: 0.474 Hom.: 14293

Bravo AF: 0.523

Asia WGS AF: 0.468 AC: 1628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.6
DANN	Benign	0.76
PhyloP100		0.026
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: rs6922711; hg19: chr6-129986792;