X-63724693-T-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_001353921.2(ARHGEF9):c.49A>G(p.Ile17Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000185 in 1,209,553 control chromosomes in the GnomAD database, including 1 homozygotes. There are 48 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0012 ( 1 hom., 30 hem., cov: 22)

Exomes 𝑓: 0.000087 ( 0 hom. 18 hem. )

Consequence

ARHGEF9
NM_001353921.2 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 2.35

Publications

1 publications found

Variant links:

Genes affected

ARHGEF9 (HGNC:14561): (Cdc42 guanine nucleotide exchange factor 9) The protein encoded by this gene is a Rho-like GTPase that switches between the active (GTP-bound) state and inactive (GDP-bound) state to regulate CDC42 and other genes. This brain-specific protein also acts as an adaptor protein for the recruitment of gephyrin and together these proteins facilitate receceptor recruitement in GABAnergic and glycinergic synapses. Defects in this gene are the cause of startle disease with epilepsy (STHEE), also known as hyperekplexia with epilepsy, as well as several other types of cognitive disability. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]

ARHGEF9 Gene-Disease associations (from GenCC):

developmental and epileptic encephalopathy, 8
Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Orphanet
X-linked complex neurodevelopmental disorder
Inheritance: XL Classification: MODERATE Submitted by: ClinGen

ARHGEF9 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.00862357).

BP6

Variant X-63724693-T-C is Benign according to our data. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63724693-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 128450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Hemizygotes in GnomAd4 at 30 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGEF9	NM_001353921.2 link	c.49A>G	p.Ile17Val	missense_variant	Exon 2 of 10	ENST00000671741.2	NP_001340850.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGEF9	ENST00000671741.2 link	c.49A>G	p.Ile17Val	missense_variant	Exon 2 of 10		NM_001353921.2	ENSP00000500715.1		A0A5F9ZHY9

Frequencies

GnomAD3 genomes

AF:

0.00116

AC:

129

AN:

111474

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00412

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000284

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000218

AC:

AN:

183125

AF XY:

0.0000740

show subpopulations

Gnomad AFR exome

AF:

0.00296

Gnomad AMR exome

AF:

0.0000365

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000865

AC:

AN:

1098023

Hom.:

Cov.:

AF XY:

0.0000495

AC XY:

AN XY:

363389

show subpopulations

African (AFR)

AF:

0.00326

AC:

AN:

26400

American (AMR)

AF:

0.0000568

AC:

AN:

35205

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19386

East Asian (EAS)

AF:

0.00

AC:

AN:

30201

South Asian (SAS)

AF:

0.00

AC:

AN:

54141

European-Finnish (FIN)

AF:

0.00

AC:

AN:

40491

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4115

European-Non Finnish (NFE)

AF:

0.00000238

AC:

AN:

841994

Other (OTH)

AF:

0.000108

AC:

AN:

46090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00116

AC:

129

AN:

111530

Hom.:

Cov.:

AF XY:

0.000890

AC XY:

AN XY:

33718

show subpopulations

African (AFR)

AF:

0.00411

AC:

126

AN:

30665

American (AMR)

AF:

0.000284

AC:

AN:

10559

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2641

East Asian (EAS)

AF:

0.00

AC:

AN:

3538

South Asian (SAS)

AF:

0.00

AC:

AN:

2603

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6035

Middle Eastern (MID)

AF:

0.00

AC:

AN:

216

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

53076

Other (OTH)

AF:

0.00

AC:

AN:

1510

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000459

Hom.:

Bravo

AF:

0.00122

ESP6500AA

AF:

0.00469

AC:

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.000222

AC:

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Dec 26, 2018

Genetic Services Laboratory, University of Chicago

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:2

Nov 12, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance:Likely benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Inborn genetic diseases

Benign:1

Dec 29, 2017

Ambry Genetics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Developmental and epileptic encephalopathy, 8

Benign:1

Jan 11, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.053

BayesDel_addAF

Benign

-0.74

BayesDel_noAF

Benign

-0.83

CADD

Benign

(source)

DANN

Benign

0.43

DEOGEN2

Benign

0.070

T;T;.;.;.;T

FATHMM_MKL

Uncertain

0.83

LIST_S2

Benign

0.81

T;T;T;T;T;T

M_CAP

Benign

0.016

MetaRNN

Benign

0.0086

T;T;T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.41

N;.;.;.;.;.

PhyloP100

2.3

PROVEAN

Benign

0.67

N;.;.;.;.;.

REVEL

Benign

0.048

Sift

Benign

1.0

T;.;.;.;.;.

Sift4G

Benign

1.0

T;T;T;T;.;.

Polyphen

0.0

B;.;.;.;.;.

Vest4

0.17

MVP

0.45

MPC

0.84

ClinPred

0.0074

GERP RS

4.0

Varity_R

0.090

gMVP

0.78

Mutation Taster

=289/11

polymorphism

(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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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