X-113664946-A-T

Position:

• chrX-113664946-A-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000468762.3(XACT):​n.294-46793T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.58 (13291 hom., 18937 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: XACT ENST00000468762.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420

Genes affected

XACT (HGNC:45056): (X active specific transcript) This gene produces a spliced long non-coding RNA that is thought to play a role in the control of X-chromosome inactivation (XCI). This transcript has been shown to specifically coat the active X chromosome in human pluripotent cells. [provided by RefSeq, Mar 2015]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
XACT	ENST00000468762.3	n.294-46793T>A		intron_variant, non_coding_transcript_variant		5
XACT	ENST00000674361.1	n.298915T>A		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.580 AC: 63844 AN: 110086 Hom.: 13292 Cov.: 22 AF XY: 0.585 AC XY: 18917 AN XY: 32360

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.700

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.595

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.580 AC: 63860 AN: 110135 Hom.: 13291 Cov.: 22 AF XY: 0.584 AC XY: 18937 AN XY: 32419

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.915

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.599

Alfa AF: 0.586 Hom.: 4414

Bravo AF: 0.577

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.30

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs761544; hg19: chrX-112908233;