rs2905403

Variant names:

• chrX-113903477-G-A
• rs2905403
• ENST00000674361.1:n.60384C>T

Variant summary

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

The ENST00000674361.1(XACT):​n.60384C>T 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 0.54 (12274 hom., 17860 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: XACT ENST00000674361.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 0 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=-0.94).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XACT	ENST00000674361.1		n.60384C>T		non_coding_transcript_exon	Exon 2 of 2
	XACT	ENST00000468762.3	TSL:5	n.293+34716C>T		intron	N/A
	XACT	ENST00000765932.1		n.359+34716C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.539 AC: 59360 AN: 110086 Hom.: 12279 Cov.: 22

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.597

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.550

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: 0.539 AC: 59368 AN: 110136 Hom.: 12274 Cov.: 22 AF XY: 0.551 AC XY: 17860 AN XY: 32438

African (AFR) AF: 0.287 AC: 8729 AN: 30421

American (AMR) AF: 0.528 AC: 5454 AN: 10331

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 1755 AN: 2618

East Asian (EAS) AF: 0.903 AC: 3147 AN: 3485

South Asian (SAS) AF: 0.766 AC: 1972 AN: 2573

European-Finnish (FIN) AF: 0.667 AC: 3818 AN: 5725

Middle Eastern (MID) AF: 0.612 AC: 128 AN: 209

European-Non Finnish (NFE) AF: 0.628 AC: 33008 AN: 52595

Other (OTH) AF: 0.555 AC: 836 AN: 1506

Alfa AF: 0.610 Hom.: 18702

Bravo AF: 0.519

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.72
PhyloP100		-0.069

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2905403;

hg19: chrX-113146754;