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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XACT	ENST00000674361.1	n.60384C>T		non_coding_transcript_exon_variant	Exon 2 of 2
XACT	ENST00000468762.3	n.293+34716C>T		intron_variant	Intron 3 of 4	5
XACT	ENST00000765932.1	n.359+34716C>T		intron_variant	Intron 3 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs2905403; hg19: chrX-113146754;