ENST00000674361.1:n.298915T>A

Variant names:

• chrX-113664946-A-T
• rs761544
• ENST00000674361.1:n.298915T>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000674361.1(XACT):​n.298915T>A variant causes a non coding transcript exon 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 ENST00000674361.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420
• Publications: 2 publications found

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

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000674361.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XACT	ENST00000674361.1		n.298915T>A		non_coding_transcript_exon	Exon 2 of 2
	XACT	ENST00000468762.3	TSL:5	n.294-46793T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.580 AC: 63844 AN: 110086 Hom.: 13292 Cov.: 22

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

African (AFR) AF: 0.488 AC: 14795 AN: 30338

American (AMR) AF: 0.578 AC: 5942 AN: 10282

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 1748 AN: 2623

East Asian (EAS) AF: 0.915 AC: 3155 AN: 3447

South Asian (SAS) AF: 0.709 AC: 1819 AN: 2565

European-Finnish (FIN) AF: 0.592 AC: 3424 AN: 5788

Middle Eastern (MID) AF: 0.717 AC: 152 AN: 212

European-Non Finnish (NFE) AF: 0.599 AC: 31548 AN: 52697

Other (OTH) AF: 0.599 AC: 903 AN: 1507

Alfa AF: 0.586 Hom.: 4414

Bravo AF: 0.577

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.30
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs761544; hg19: chrX-112908233;