4-85994770-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001025616.3(ARHGAP24):c.1116G>A(p.Arg372Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 1,613,854 control chromosomes in the GnomAD database, including 45,398 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.21 ( 3611 hom., cov: 31)

Exomes 𝑓: 0.23 ( 41787 hom. )

Consequence

ARHGAP24
NM_001025616.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.0780

Publications

9 publications found

Variant links:

Genes affected

ARHGAP24 (HGNC:25361): (Rho GTPase activating protein 24) This gene encodes a Rho-GTPase activating protein, which is specific for the small GTPase family member Rac. Binding of the encoded protein by filamin A targets it to sites of membrane protrusion, where it antognizes Rac. This results in suppression of lamellae formation and promotion of retraction to regulate cell polarity. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]

ARHGAP24 links:

MAPK10 (HGNC:6872): (mitogen-activated protein kinase 10) The protein encoded by this gene is a member of the MAP kinase family. MAP kinases act as integration points for multiple biochemical signals, and thus are involved in a wide variety of cellular processes, such as proliferation, differentiation, transcription regulation and development. This kinase is specifically expressed in a subset of neurons in the nervous system, and is activated by threonine and tyrosine phosphorylation. Targeted deletion of this gene in mice suggests that it may have a role in stress-induced neuronal apoptosis. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. A recent study provided evidence for translational readthrough in this gene, and expression of an additional C-terminally extended isoform via the use of an alternative in-frame translation termination codon. [provided by RefSeq, Dec 2017]

MAPK10 Gene-Disease associations (from GenCC):

Lennox-Gastaut syndrome
Inheritance: AD Classification: LIMITED Submitted by: G2P

MAPK10 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 4-85994770-G-A is Benign according to our data. Variant chr4-85994770-G-A is described in ClinVar as [Benign]. Clinvar id is 1274074.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.078 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGAP24	NM_001025616.3 link	c.1116G>A	p.Arg372Arg	synonymous_variant	Exon 9 of 10	ENST00000395184.6	NP_001020787.2	Q8N264-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP24	ENST00000395184.6 link	c.1116G>A	p.Arg372Arg	synonymous_variant	Exon 9 of 10	2	NM_001025616.3	ENSP00000378611.1		Q8N264-1

Frequencies

GnomAD3 genomes

AF:

0.210

AC:

31854

AN:

151886

Hom.:

3618

Cov.:

show subpopulations

Gnomad AFR

AF:

0.139

Gnomad AMI

AF:

0.145

Gnomad AMR

AF:

0.270

Gnomad ASJ

AF:

0.188

Gnomad EAS

AF:

0.283

Gnomad SAS

AF:

0.395

Gnomad FIN

AF:

0.236

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.219

Gnomad OTH

AF:

0.199

GnomAD2 exomes

AF:

0.257

AC:

64471

AN:

251178

AF XY:

0.260

show subpopulations

Gnomad AFR exome

AF:

0.130

Gnomad AMR exome

AF:

0.341

Gnomad ASJ exome

AF:

0.201

Gnomad EAS exome

AF:

0.286

Gnomad FIN exome

AF:

0.238

Gnomad NFE exome

AF:

0.220

Gnomad OTH exome

AF:

0.234

GnomAD4 exome

AF:

0.233

AC:

340856

AN:

1461850

Hom.:

41787

Cov.:

AF XY:

0.238

AC XY:

172769

AN XY:

727234

show subpopulations

African (AFR)

AF:

0.133

AC:

4437

AN:

33474

American (AMR)

AF:

0.331

AC:

14799

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.192

AC:

5015

AN:

26134

East Asian (EAS)

AF:

0.281

AC:

11156

AN:

39700

South Asian (SAS)

AF:

0.384

AC:

33147

AN:

86258

European-Finnish (FIN)

AF:

0.234

AC:

12477

AN:

53416

Middle Eastern (MID)

AF:

0.217

AC:

1253

AN:

5768

European-Non Finnish (NFE)

AF:

0.220

AC:

244552

AN:

1111986

Other (OTH)

AF:

0.232

AC:

14020

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

18610

37219

55829

74438

93048

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.210

AC:

31863

AN:

152004

Hom.:

3611

Cov.:

AF XY:

0.217

AC XY:

16125

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.139

AC:

5767

AN:

41472

American (AMR)

AF:

0.269

AC:

4112

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.188

AC:

651

AN:

3468

East Asian (EAS)

AF:

0.282

AC:

1450

AN:

5138

South Asian (SAS)

AF:

0.394

AC:

1897

AN:

4812

European-Finnish (FIN)

AF:

0.236

AC:

2491

AN:

10558

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.219

AC:

14893

AN:

67960

Other (OTH)

AF:

0.198

AC:

418

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1242

2484

3727

4969

6211

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.184

Hom.:

2297

Bravo

AF:

0.206

Asia WGS

AF:

0.350

AC:

1213

AN:

3478

EpiCase

AF:

0.218

EpiControl

AF:

0.214

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Feb 02, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Nov 10, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

5.7

(source)

DANN

Benign

0.57

PhyloP100

0.078

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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4-85994770-G-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over