rs56110425

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001353921.2(ARHGEF9):ā€‹c.1225A>Gā€‹(p.Ile409Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000149 in 1,209,578 control chromosomes in the GnomAD database, including 1 homozygotes. There are 49 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 (ā˜…ā˜…).

Frequency

Genomes: š‘“ 0.00018 ( 1 hom., 2 hem., cov: 22)
Exomes š‘“: 0.00015 ( 0 hom. 47 hem. )

Consequence

ARHGEF9
NM_001353921.2 missense

Scores

1
16

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.914
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.021755159).
BP6
Variant X-63655590-T-C is Benign according to our data. Variant chrX-63655590-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 465075.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-63655590-T-C is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.000179 (20/111732) while in subpopulation AMR AF= 0.000286 (3/10507). AF 95% confidence interval is 0.00013. There are 1 homozygotes in gnomad4. There are 2 alleles in male gnomad4 subpopulation. Median coverage is 22. This position pass quality control queck.
BS2
High Hemizygotes in GnomAd4 at 2 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ARHGEF9NM_001353921.2 linkuse as main transcriptc.1225A>G p.Ile409Val missense_variant 8/10 ENST00000671741.2 NP_001340850.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ARHGEF9ENST00000671741.2 linkuse as main transcriptc.1225A>G p.Ile409Val missense_variant 8/10 NM_001353921.2 ENSP00000500715.1 A0A5F9ZHY9

Frequencies

GnomAD3 genomes
AF:
0.000179
AC:
20
AN:
111732
Hom.:
1
Cov.:
22
AF XY:
0.0000590
AC XY:
2
AN XY:
33912
show subpopulations
Gnomad AFR
AF:
0.000130
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000286
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:
0.000226
Gnomad OTH
AF:
0.000673
GnomAD3 exomes
AF:
0.000296
AC:
54
AN:
182738
Hom.:
0
AF XY:
0.000237
AC XY:
16
AN XY:
67484
show subpopulations
Gnomad AFR exome
AF:
0.0000760
Gnomad AMR exome
AF:
0.000987
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000258
Gnomad OTH exome
AF:
0.00111
GnomAD4 exome
AF:
0.000146
AC:
160
AN:
1097846
Hom.:
0
Cov.:
31
AF XY:
0.000129
AC XY:
47
AN XY:
363372
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000796
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000132
Gnomad4 OTH exome
AF:
0.000369
GnomAD4 genome
AF:
0.000179
AC:
20
AN:
111732
Hom.:
1
Cov.:
22
AF XY:
0.0000590
AC XY:
2
AN XY:
33912
show subpopulations
Gnomad4 AFR
AF:
0.000130
Gnomad4 AMR
AF:
0.000286
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000226
Gnomad4 OTH
AF:
0.000673
Alfa
AF:
0.000263
Hom.:
10
Bravo
AF:
0.000219
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000149
AC:
1
ExAC
AF:
0.000321
AC:
39
EpiCase
AF:
0.000437
EpiControl
AF:
0.000356

ClinVar

Significance: Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Developmental and epileptic encephalopathy, 8 Benign:2
Likely benign, criteria provided, single submitterclinical testingFulgent Genetics, Fulgent GeneticsSep 01, 2021- -
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 11, 2024- -
ARHGEF9-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesMay 10, 2023This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenFeb 01, 2023ARHGEF9: BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.058
BayesDel_addAF
Benign
-0.60
T
BayesDel_noAF
Benign
-0.70
CADD
Benign
14
DANN
Benign
0.46
DEOGEN2
Benign
0.20
T;T;.;T;T;T;T;T;T;.;.;T;.;T;T;.;T;.;T;T;.
FATHMM_MKL
Benign
0.71
D
LIST_S2
Benign
0.81
T;T;T;T;.;T;.;.;.;T;T;.;T;.;.;T;.;T;T;T;T
M_CAP
Benign
0.0080
T
MetaRNN
Benign
0.022
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.76
T
MutationAssessor
Benign
-0.46
N;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.
PrimateAI
Uncertain
0.52
T
PROVEAN
Benign
0.34
N;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;N;.;.;.;.
REVEL
Benign
0.10
Sift
Benign
1.0
T;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;T;.;.;.;.
Sift4G
Benign
1.0
T;T;T;.;.;.;.;.;.;T;T;T;.;.;.;.;T;T;.;.;.
Polyphen
0.0
B;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.
Vest4
0.12
MVP
0.59
MPC
0.84
ClinPred
0.0037
T
GERP RS
1.9
Varity_R
0.034
gMVP
0.50

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
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: rs56110425; hg19: chrX-62875470; API