rs3007183

Positions:

• chrX-113908725-A-G

Variant summary

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

The ENST00000468762.3(XACT):​n.293+29468T>C 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 0.55 (12681 hom., 18080 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: XACT ENST00000468762.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

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=-0.91).

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.293+29468T>C		intron_variant, non_coding_transcript_variant		5
XACT	ENST00000674361.1	n.55136T>C		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.553 AC: 60739 AN: 109887 Hom.: 12685 Cov.: 22 AF XY: 0.561 AC XY: 18053 AN XY: 32205

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.581

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.558

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: 0.553 AC: 60754 AN: 109940 Hom.: 12681 Cov.: 22 AF XY: 0.560 AC XY: 18080 AN XY: 32268

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.898

Gnomad4 SAS AF: 0.769

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.563

Alfa AF: 0.625 Hom.: 17012

Bravo AF: 0.536

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3007183; hg19: chrX-113152000;