rs9375644

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_033515.3(ARHGAP18):​c.617-1334G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 151,940 control chromosomes in the GnomAD database, including 22,449 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 0.53 ( 22449 hom., cov: 31)

Consequence

ARHGAP18
NM_033515.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.87
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ARHGAP18NM_033515.3 linkuse as main transcriptc.617-1334G>A intron_variant ENST00000368149.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ARHGAP18ENST00000368149.3 linkuse as main transcriptc.617-1334G>A intron_variant 1 NM_033515.3 P1Q8N392-1

Frequencies

GnomAD3 genomes
AF:
0.530
AC:
80448
AN:
151822
Hom.:
22405
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.706
Gnomad AMI
AF:
0.316
Gnomad AMR
AF:
0.463
Gnomad ASJ
AF:
0.423
Gnomad EAS
AF:
0.339
Gnomad SAS
AF:
0.402
Gnomad FIN
AF:
0.471
Gnomad MID
AF:
0.545
Gnomad NFE
AF:
0.479
Gnomad OTH
AF:
0.534
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.530
AC:
80556
AN:
151940
Hom.:
22449
Cov.:
31
AF XY:
0.526
AC XY:
39076
AN XY:
74254
show subpopulations
Gnomad4 AFR
AF:
0.706
Gnomad4 AMR
AF:
0.463
Gnomad4 ASJ
AF:
0.423
Gnomad4 EAS
AF:
0.339
Gnomad4 SAS
AF:
0.402
Gnomad4 FIN
AF:
0.471
Gnomad4 NFE
AF:
0.479
Gnomad4 OTH
AF:
0.538
Alfa
AF:
0.488
Hom.:
30735
Bravo
AF:
0.537
Asia WGS
AF:
0.411
AC:
1426
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
0.36
DANN
Benign
0.56

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9375644; hg19: chr6-129952001; API