X-113908725-A-G

Variant names:

• chrX-113908725-A-G
• rs3007183
• ENST00000674361.1:n.55136T>C

Variant summary

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

The ENST00000674361.1(XACT):​n.55136T>C 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 0.55 (12681 hom., 18080 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: XACT ENST00000674361.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• 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=-0.91).

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.55136T>C		non_coding_transcript_exon	Exon 2 of 2
	XACT	ENST00000468762.3	TSL:5	n.293+29468T>C		intron	N/A
	XACT	ENST00000765932.1		n.359+29468T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.553 AC: 60739 AN: 109887 Hom.: 12685 Cov.: 22

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

African (AFR) AF: 0.329 AC: 9972 AN: 30334

American (AMR) AF: 0.534 AC: 5486 AN: 10269

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 1750 AN: 2616

East Asian (EAS) AF: 0.898 AC: 3108 AN: 3461

South Asian (SAS) AF: 0.769 AC: 1971 AN: 2562

European-Finnish (FIN) AF: 0.682 AC: 3947 AN: 5784

Middle Eastern (MID) AF: 0.596 AC: 124 AN: 208

European-Non Finnish (NFE) AF: 0.629 AC: 33032 AN: 52534

Other (OTH) AF: 0.563 AC: 842 AN: 1496

Alfa AF: 0.605 Hom.: 24094

Bravo AF: 0.536

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs3007183; hg19: chrX-113152000;