Variant chrX-18425432-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The variant allele was found at a frequency of 0.00326 in 113,139 control chromosomes in the GnomAD database, including 1 homozygotes. There are 102 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0033 ( 1 hom., 102 hem., cov: 25)

Consequence

intergenic_region

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: -0.0410

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant X-18425432-C-G is Benign according to our data. Variant chrX-18425432-C-G is described in ClinVar as [Benign]. Clinvar id is 189539.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAd4 at 102 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.18425432C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.00327

AC:

370

AN:

113089

Hom.:

Cov.:

AF XY:

0.00289

AC XY:

102

AN XY:

35239

show subpopulations

Gnomad AFR

AF:

0.000674

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00343

Gnomad ASJ

AF:

0.0165

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000717

Gnomad FIN

AF:

0.00238

Gnomad MID

AF:

0.0167

Gnomad NFE

AF:

0.00429

Gnomad OTH

AF:

0.0117

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.00326

AC:

369

AN:

113139

Hom.:

Cov.:

AF XY:

0.00289

AC XY:

102

AN XY:

35299

show subpopulations

Gnomad4 AFR

AF:

0.000672

Gnomad4 AMR

AF:

0.00342

Gnomad4 ASJ

AF:

0.0165

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000719

Gnomad4 FIN

AF:

0.00238

Gnomad4 NFE

AF:

0.00429

Gnomad4 OTH

AF:

0.0116

Alfa

AF:

0.00114

Hom.:

Bravo

AF:

0.00339

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, no assertion criteria provided

curation

RettBASE

May 09, 2014

Found in normal population -

CDKL5 disorder

Benign:1

Benign, criteria provided, single submitter

curation

Centre for Population Genomics, CPG

Jun 28, 2024

This variant has been collected from RettBASE and curated to current modified ACMG/AMP criteria. Based on the classification scheme defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like Disorders Specifications to the ACMG/AMP Variant Interpretation Guidelines VCEP 3.0, this variant is classified as benign. At least the following criteria are met: The allele frequency of this variant in at least one population in gnomAD v3 is higher than the 0.03% threshold defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like Disorders VCEP 3.0 (BA1). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.9

DANN

Benign

0.49

Splicing

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