Genetic Variant XIST:n.9725C>T (chrX-73842999-G-A) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The ENST00000429829.6(XIST):n.9725C>T 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 0.00271 in 556,789 control chromosomes in the GnomAD database, including 3 homozygotes. There are 532 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0022 ( 1 hom., 72 hem., cov: 22)

Exomes 𝑓: 0.0028 ( 2 hom. 460 hem. )

Consequence

XIST
ENST00000429829.6 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.00800

Variant links:

Genes affected

XIST (HGNC:12810): (X inactive specific transcript) X inactivation is an early developmental process in mammalian females that transcriptionally silences one of the pair of X chromosomes, thus providing dosage equivalence between males and females. The process is regulated by several factors, including a region of chromosome X called the X inactivation center (XIC). The XIC comprises several non-coding and protein-coding genes, and this gene was the first non-coding gene identified within the XIC. This gene is expressed exclusively from the XIC of the inactive X chromosome, and is essential for the initiation and spread of X-inactivation. The transcript is a spliced RNA. Alternatively spliced transcript variants have been identified, but their full length sequences have not been determined. Mutations in the XIST promoter cause familial skewed X inactivation. [provided by RefSeq, Apr 2012]

XIST links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant X-73842999-G-A is Benign according to our data. Variant chrX-73842999-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3040456.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Hemizygotes in GnomAd4 at 72 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
XIST	NR_001564.3 link	n.9716C>T	non_coding_transcript_exon_variant	Exon 1 of 6
XIST	NR_190997.1 link	n.9716C>T	non_coding_transcript_exon_variant	Exon 1 of 8
XIST	NR_190999.1 link	n.9716C>T	non_coding_transcript_exon_variant	Exon 1 of 7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
XIST	ENST00000429829.6 link	n.9725C>T	non_coding_transcript_exon_variant	Exon 1 of 6	1
XIST	ENST00000648607.1 link	n.1210C>T	non_coding_transcript_exon_variant	Exon 1 of 6
XIST	ENST00000648991.1 link	n.1085C>T	non_coding_transcript_exon_variant	Exon 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.00222

AC:

247

AN:

111421

Hom.:

Cov.:

AF XY:

0.00214

AC XY:

AN XY:

33611

show subpopulations

Gnomad AFR

AF:

0.000359

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00872

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000828

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00390

Gnomad OTH

AF:

0.000668

GnomAD3 exomes

AF:

0.00263

AC:

441

AN:

167434

Hom.:

AF XY:

0.00261

AC XY:

166

AN XY:

63594

show subpopulations

Gnomad AFR exome

AF:

0.000360

Gnomad AMR exome

AF:

0.0000736

Gnomad ASJ exome

AF:

0.00589

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00204

Gnomad NFE exome

AF:

0.00473

Gnomad OTH exome

AF:

0.00233

GnomAD4 exome

AF:

0.00284

AC:

1264

AN:

445321

Hom.:

Cov.:

AF XY:

0.00275

AC XY:

460

AN XY:

167419

show subpopulations

Gnomad4 AFR exome

AF:

0.000501

Gnomad4 AMR exome

AF:

0.0000873

Gnomad4 ASJ exome

AF:

0.00558

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000237

Gnomad4 FIN exome

AF:

0.00165

Gnomad4 NFE exome

AF:

0.00419

Gnomad4 OTH exome

AF:

0.00189

GnomAD4 genome

AF:

0.00222

AC:

247

AN:

111468

Hom.:

Cov.:

AF XY:

0.00214

AC XY:

AN XY:

33668

show subpopulations

Gnomad4 AFR

AF:

0.000358

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00872

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000828

Gnomad4 NFE

AF:

0.00390

Gnomad4 OTH

AF:

0.000660

Alfa

AF:

0.00338

Hom.:

Bravo

AF:

0.00188

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

XIST-related disorder

Benign:1

Apr 18, 2019

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.2

DANN

Benign

0.43

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.1

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