chrX-100296444-G-C

Position:

chrX-100296444-G-C

Variant summary

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

The NM_001184880.2(PCDH19):c.3280C>G(p.Leu1094Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00247 in 1,209,488 control chromosomes in the GnomAD database, including 2 homozygotes. There are 951 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0015 ( 0 hom., 46 hem., cov: 22)

Exomes 𝑓: 0.0026 ( 2 hom. 905 hem. )

Consequence

PCDH19
NM_001184880.2 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.83

Variant links:

Genes affected

PCDH19 (HGNC:14270): (protocadherin 19) The protein encoded by this gene is a member of the delta-2 protocadherin subclass of the cadherin superfamily. The encoded protein is thought to be a calcium-dependent cell-adhesion protein that is primarily expressed in the brain. Mutations in this gene on human chromosome X are associated with sporadic infantile epileptic encephalopathy and to a female-restricted form of epilepsy (EFMR; also known as PCDH19RE). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]

PCDH19 links:

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=0.0055009425).

BP6

Variant X-100296444-G-C is Benign according to our data. Variant chrX-100296444-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 138593.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-100296444-G-C is described in Lovd as [Likely_benign]. Variant chrX-100296444-G-C is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0015 (167/111375) while in subpopulation NFE AF= 0.00232 (123/53088). AF 95% confidence interval is 0.00198. There are 0 homozygotes in gnomad4. There are 46 alleles in male gnomad4 subpopulation. Median coverage is 22. This position pass quality control queck.

BS2

High Hemizygotes in GnomAd4 at 46 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
PCDH19	NM_001184880.2 linkuse as main transcript	c.3280C>G	p.Leu1094Val	missense_variant	6/6	ENST00000373034.8	NP_001171809.1
PCDH19	NM_001105243.2 linkuse as main transcript	c.3139C>G	p.Leu1047Val	missense_variant	5/5		NP_001098713.1
PCDH19	NM_020766.3 linkuse as main transcript	c.3136C>G	p.Leu1046Val	missense_variant	5/5		NP_065817.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCDH19	ENST00000373034.8 linkuse as main transcript	c.3280C>G	p.Leu1094Val	missense_variant	6/6	1	NM_001184880.2	ENSP00000362125	A1	Q8TAB3-1
PCDH19	ENST00000255531.8 linkuse as main transcript	c.3139C>G	p.Leu1047Val	missense_variant	5/5	1		ENSP00000255531	P5	Q8TAB3-2
PCDH19	ENST00000420881.6 linkuse as main transcript	c.3136C>G	p.Leu1046Val	missense_variant	5/5	1		ENSP00000400327	A1	Q8TAB3-3

Frequencies

GnomAD3 genomes

AF:

0.00150

AC:

167

AN:

111318

Hom.:

Cov.:

AF XY:

0.00137

AC XY:

AN XY:

33498

show subpopulations

Gnomad AFR

AF:

0.000262

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00219

Gnomad ASJ

AF:

0.00304

Gnomad EAS

AF:

0.000564

Gnomad SAS

AF:

0.000391

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00418

Gnomad NFE

AF:

0.00232

Gnomad OTH

AF:

0.000669

GnomAD3 exomes

AF:

0.00148

AC:

269

AN:

181515

Hom.:

AF XY:

0.00150

AC XY:

101

AN XY:

67467

show subpopulations

Gnomad AFR exome

AF:

0.000161

Gnomad AMR exome

AF:

0.000402

Gnomad ASJ exome

AF:

0.00214

Gnomad EAS exome

AF:

0.000443

Gnomad SAS exome

AF:

0.00110

Gnomad FIN exome

AF:

0.000189

Gnomad NFE exome

AF:

0.00246

Gnomad OTH exome

AF:

0.00224

GnomAD4 exome

AF:

0.00256

AC:

2815

AN:

1098113

Hom.:

Cov.:

AF XY:

0.00249

AC XY:

905

AN XY:

363469

show subpopulations

Gnomad4 AFR exome

AF:

0.000227

Gnomad4 AMR exome

AF:

0.000540

Gnomad4 ASJ exome

AF:

0.00201

Gnomad4 EAS exome

AF:

0.00103

Gnomad4 SAS exome

AF:

0.000997

Gnomad4 FIN exome

AF:

0.0000987

Gnomad4 NFE exome

AF:

0.00302

Gnomad4 OTH exome

AF:

0.00230

GnomAD4 genome

AF:

0.00150

AC:

167

AN:

111375

Hom.:

Cov.:

AF XY:

0.00137

AC XY:

AN XY:

33565

show subpopulations

Gnomad4 AFR

AF:

0.000261

Gnomad4 AMR

AF:

0.00218

Gnomad4 ASJ

AF:

0.00304

Gnomad4 EAS

AF:

0.000566

Gnomad4 SAS

AF:

0.000392

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00232

Gnomad4 OTH

AF:

0.000660

Alfa

AF:

0.00223

Hom.:

Bravo

AF:

0.00171

TwinsUK

AF:

0.00270

AC:

ALSPAC

AF:

0.00346

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.00351

AC:

ExAC

AF:

0.00150

AC:

181

EpiCase

AF:

0.00202

EpiControl

AF:

0.00279

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:12

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 14, 2013	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Mar 03, 2017	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Feb 23, 2015	- -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -

Developmental and epileptic encephalopathy, 9

Benign:4

Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -
Likely benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Oct 09, 2023	- -
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	Center for Human Genetics, Inc, Center for Human Genetics, Inc	Nov 01, 2016	- -

not provided

Benign:3

Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Likely benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Inborn genetic diseases

Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

May 22, 2018

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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.063

BayesDel_addAF

Benign

-0.69

BayesDel_noAF

Benign

-0.77

CADD

Benign

DANN

Benign

0.25

DEOGEN2

Benign

0.020

.;T;.

FATHMM_MKL

Benign

0.72

LIST_S2

Benign

0.67

T;T;T

M_CAP

Uncertain

0.24

MetaRNN

Benign

0.0055

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.34

.;N;.

MutationTaster

Benign

0.94

N;N;N

PrimateAI

Benign

0.33

PROVEAN

Benign

0.010

N;N;N

REVEL

Benign

0.086

Sift

Benign

0.67

T;T;T

Sift4G

Benign

0.92

T;T;T

Polyphen

0.0

.;B;B

Vest4

0.094

MVP

0.37

MPC

0.51

ClinPred

0.0036

GERP RS

1.4

Varity_R

0.079

gMVP

0.21

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