rs3007183

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).

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.55136T>C		non_coding_transcript_exon_variant	Exon 2 of 2
XACT	ENST00000468762.3	n.293+29468T>C		intron_variant	Intron 3 of 4	5
XACT	ENST00000765932.1	n.359+29468T>C		intron_variant	Intron 3 of 3

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 v4.3

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;