6-129597865-T-C

Variant names:

• chr6-129597865-T-C
• rs10499162
• NM_033515.3:c.1713+1351A>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.1713+1351A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 151,972 control chromosomes in the GnomAD database, including 1,385 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 0.13 (1385 hom., cov: 32)
• Consequence: ARHGAP18 NM_033515.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 7 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGAP18	NM_033515.3	c.1713+1351A>G		intron_variant	Intron 12 of 14	ENST00000368149.3	NP_277050.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP18	ENST00000368149.3	c.1713+1351A>G		intron_variant	Intron 12 of 14	1	NM_033515.3	ENSP00000357131.2
ARHGAP18	ENST00000463225.1	n.91+1006A>G		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19883 AN: 151854 Hom.: 1383 Cov.: 32

Gnomad AFR AF: 0.0905

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0606

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.131 AC: 19898 AN: 151972 Hom.: 1385 Cov.: 32 AF XY: 0.134 AC XY: 9918 AN XY: 74280

African (AFR) AF: 0.0905 AC: 3759 AN: 41528

American (AMR) AF: 0.181 AC: 2763 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 389 AN: 3470

East Asian (EAS) AF: 0.128 AC: 661 AN: 5182

South Asian (SAS) AF: 0.0600 AC: 289 AN: 4816

European-Finnish (FIN) AF: 0.193 AC: 2037 AN: 10576

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9567 AN: 67838

Other (OTH) AF: 0.145 AC: 306 AN: 2112

Alfa AF: 0.128 Hom.: 567

Bravo AF: 0.130

Asia WGS AF: 0.122 AC: 424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.69
PhyloP100		-0.035
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: rs10499162; hg19: chr6-129919010; COSMIC: COSV63763757; COSMIC: COSV63763757;