rs145644275

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2

The NM_004463.3(FGD1):c.395G>A(p.Arg132Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00196 in 1,209,766 control chromosomes in the GnomAD database, including 1 homozygotes. There are 720 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0012 ( 0 hom., 43 hem., cov: 23)

Exomes 𝑓: 0.0020 ( 1 hom. 677 hem. )

Consequence

FGD1
NM_004463.3 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:12

Conservation

PhyloP100: 4.86

Variant links:

Genes affected

FGD1 (HGNC:3663): (FYVE, RhoGEF and PH domain containing 1) This gene encodes a protein that contains Dbl (DH) and pleckstrin (PH) homology domains and is similar to the Rho family of small GTP-binding proteins. The encoded protein specifically binds to the Rho family GTPase Cdc42Hs and can stimulate the GDP-GTP exchange of the isoprenylated form of Cdc42Hs. It also stimulates the mitogen activated protein kinase cascade leading to c-Jun kinase SAPK/JNK1 activation. Defects in this gene are the cause of the faciogenital dysplasia in Aarskog-Scott syndrome and a syndromatic form of X-linked cognitive disability. [provided by RefSeq, Jul 2017]

FGD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

PP2

Missense variant where missense usually causes diseases, FGD1

BP4

Computational evidence support a benign effect (MetaRNN=0.0061568916).

BP6

Variant X-54471400-C-T is Benign according to our data. Variant chrX-54471400-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 95092.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-54471400-C-T is described in Lovd as [Likely_benign]. Variant chrX-54471400-C-T is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00124 (140/112605) while in subpopulation NFE AF= 0.00206 (110/53301). AF 95% confidence interval is 0.00175. There are 0 homozygotes in gnomad4. There are 43 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.

BS2

High Hemizygotes in GnomAd at 43 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FGD1	NM_004463.3 linkuse as main transcript	c.395G>A	p.Arg132Gln	missense_variant	2/18	ENST00000375135.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGD1	ENST00000375135.4 linkuse as main transcript	c.395G>A	p.Arg132Gln	missense_variant	2/18	1	NM_004463.3	P1

Frequencies

GnomAD3 genomes

AF:

0.00124

AC:

140

AN:

112555

Hom.:

Cov.:

AF XY:

0.00124

AC XY:

AN XY:

34709

show subpopulations

Gnomad AFR

AF:

0.000323

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000938

Gnomad ASJ

AF:

0.000753

Gnomad EAS

AF:

0.000280

Gnomad SAS

AF:

0.000365

Gnomad FIN

AF:

0.000483

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00206

Gnomad OTH

AF:

0.00198

GnomAD3 exomes

AF:

0.00132

AC:

242

AN:

183402

Hom.:

AF XY:

0.00124

AC XY:

AN XY:

67840

show subpopulations

Gnomad AFR exome

AF:

0.000380

Gnomad AMR exome

AF:

0.000729

Gnomad ASJ exome

AF:

0.000935

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00100

Gnomad NFE exome

AF:

0.00227

Gnomad OTH exome

AF:

0.00177

GnomAD4 exome

AF:

0.00204

AC:

2236

AN:

1097161

Hom.:

Cov.:

AF XY:

0.00187

AC XY:

677

AN XY:

362863

show subpopulations

Gnomad4 AFR exome

AF:

0.000190

Gnomad4 AMR exome

AF:

0.000909

Gnomad4 ASJ exome

AF:

0.000826

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000111

Gnomad4 FIN exome

AF:

0.00116

Gnomad4 NFE exome

AF:

0.00245

Gnomad4 OTH exome

AF:

0.00130

GnomAD4 genome

AF:

0.00124

AC:

140

AN:

112605

Hom.:

Cov.:

AF XY:

0.00124

AC XY:

AN XY:

34769

show subpopulations

Gnomad4 AFR

AF:

0.000322

Gnomad4 AMR

AF:

0.000937

Gnomad4 ASJ

AF:

0.000753

Gnomad4 EAS

AF:

0.000281

Gnomad4 SAS

AF:

0.000366

Gnomad4 FIN

AF:

0.000483

Gnomad4 NFE

AF:

0.00206

Gnomad4 OTH

AF:

0.00195

Alfa

AF:

0.00198

Hom.:

Bravo

AF:

0.00122

TwinsUK

AF:

0.00108

AC:

ALSPAC

AF:

0.00381

AC:

ESP6500AA

AF:

0.000522

AC:

ESP6500EA

AF:

0.00312

AC:

ExAC

AF:

0.00135

AC:

164

EpiCase

AF:

0.00234

EpiControl

AF:

0.00249

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:12

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:5

Likely benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Jun 14, 2017	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 03, 2024	- -
Likely benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -

Aarskog syndrome

Benign:3

Likely benign, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Likely benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Aug 11, 2021	- -

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Oct 29, 2013	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -

Inborn genetic diseases

Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 07, 2016

This alteration is classified as 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. -

FGD1-related disorder

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Aug 07, 2019

This 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). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.50

BayesDel_noAF

Benign

-0.49

Cadd

Uncertain

Dann

Pathogenic

1.0

DEOGEN2

Benign

0.10

FATHMM_MKL

Uncertain

0.88

LIST_S2

Benign

0.85

M_CAP

Benign

0.044

MetaRNN

Benign

0.0062

MetaSVM

Benign

-0.61

MutationAssessor

Benign

0.34

MutationTaster

Benign

0.51

PrimateAI

Benign

0.41

PROVEAN

Benign

-0.80

REVEL

Benign

0.091

Sift

Uncertain

0.011

Sift4G

Benign

0.26

Polyphen

0.50

Vest4

0.14

MVP

0.58

MPC

0.33

ClinPred

0.015

GERP RS

4.9

Varity_R

0.22

gMVP

0.080

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over