Variant X-73827076-ATC-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2

The ENST00000429829.6(XIST):n.12823_12824delGA variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000368 in 556,386 control chromosomes in the GnomAD database, including 3 homozygotes. There are 61 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.00050 ( 3 hom., 7 hem., cov: 22)

Exomes 𝑓: 0.00034 ( 0 hom. 54 hem. )

Consequence

XIST
ENST00000429829.6 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.754

Variant links:

Genes affected

XIST (HGNC:):

XIST links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP6

Variant X-73827076-ATC-A is Benign according to our data. Variant chrX-73827076-ATC-A is described in ClinVar as [Likely_benign]. Clinvar id is 3042415.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
XIST	NR_001564.2 linkuse as main transcript	n.12853_12854delGA		non_coding_transcript_exon_variant	6/6
TSIX	NR_003255.2 linkuse as main transcript	n.34874_34875delCT		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
XIST	ENST00000429829.6 linkuse as main transcript	n.12823_12824delGA	non_coding_transcript_exon_variant	6/6	1
XIST	ENST00000421322.3 linkuse as main transcript	n.1995_1996delGA	non_coding_transcript_exon_variant	6/7	2
XIST	ENST00000434839.3 linkuse as main transcript	n.1525_1526delGA	non_coding_transcript_exon_variant	5/6	5

Frequencies

GnomAD3 genomes

AF:

0.000496

AC:

AN:

110881

Hom.:

Cov.:

AF XY:

0.000211

AC XY:

AN XY:

33099

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00241

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00737

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000189

Gnomad OTH

AF:

0.00202

GnomAD3 exomes

AF:

0.000531

AC:

AN:

165836

Hom.:

AF XY:

0.000411

AC XY:

AN XY:

63268

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000368

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00567

Gnomad SAS exome

AF:

0.000371

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00116

GnomAD4 exome

AF:

0.000337

AC:

150

AN:

445451

Hom.:

AF XY:

0.000322

AC XY:

AN XY:

167511

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000291

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00316

Gnomad4 SAS exome

AF:

0.000190

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000156

Gnomad4 OTH exome

AF:

0.00205

GnomAD4 genome

AF:

0.000496

AC:

AN:

110935

Hom.:

Cov.:

AF XY:

0.000211

AC XY:

AN XY:

33161

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00240

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00739

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000189

Gnomad4 OTH

AF:

0.00199

Alfa

AF:

0.0000712

Hom.:

Bravo

AF:

0.000298

Asia WGS

AF:

0.00995

AC:

AN:

2522

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

TSIX-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jun 26, 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

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