Variant X-73821427-T-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000429829.6(XIST):n.18474A>C 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 0.000545 in 556,257 control chromosomes in the GnomAD database, including 1 homozygotes. There are 104 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 0.00064 ( 0 hom., 30 hem., cov: 23)

Exomes 𝑓: 0.00052 ( 1 hom. 74 hem. )

Consequence

XIST
ENST00000429829.6 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.164

Variant links:

Genes affected

XIST (HGNC:):

XIST links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant X-73821427-T-G is Benign according to our data. Variant chrX-73821427-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 3041021.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Hemizygotes in GnomAd4 at 30 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
XIST	NR_001564.2 linkuse as main transcript	n.18504A>C		non_coding_transcript_exon_variant	6/6
TSIX	NR_003255.2 linkuse as main transcript	n.29223T>G		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
XIST	ENST00000429829.6 linkuse as main transcript	n.18474A>C	non_coding_transcript_exon_variant	6/6	1
TSIX	ENST00000604411.1 linkuse as main transcript	n.29223T>G	non_coding_transcript_exon_variant	1/1	6
XIST	ENST00000650366.1 linkuse as main transcript	n.11812A>C	non_coding_transcript_exon_variant	5/5

Frequencies

GnomAD3 genomes

AF:

0.000638

AC:

AN:

112798

Hom.:

Cov.:

AF XY:

0.000858

AC XY:

AN XY:

34948

show subpopulations

Gnomad AFR

AF:

0.0000967

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000187

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00337

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000843

Gnomad OTH

AF:

0.000656

GnomAD3 exomes

AF:

0.000426

AC:

AN:

159773

Hom.:

AF XY:

0.000501

AC XY:

AN XY:

57827

show subpopulations

Gnomad AFR exome

AF:

0.0000926

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00273

Gnomad NFE exome

AF:

0.000624

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000521

AC:

231

AN:

443407

Hom.:

Cov.:

AF XY:

0.000447

AC XY:

AN XY:

165657

show subpopulations

Gnomad4 AFR exome

AF:

0.0000715

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00317

Gnomad4 NFE exome

AF:

0.000498

Gnomad4 OTH exome

AF:

0.000525

GnomAD4 genome

AF:

0.000638

AC:

AN:

112850

Hom.:

Cov.:

AF XY:

0.000857

AC XY:

AN XY:

35010

show subpopulations

Gnomad4 AFR

AF:

0.0000964

Gnomad4 AMR

AF:

0.000187

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00337

Gnomad4 NFE

AF:

0.000843

Gnomad4 OTH

AF:

0.000648

Alfa

AF:

0.00165

Hom.:

Bravo

AF:

0.000295

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

Aug 30, 2023

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

-0.82

CADD

Benign

2.3

DANN

Benign

0.47

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