rs2905404

Variant names:

• chrX-113898791-G-A
• rs2905404
• ENST00000674361.1:n.65070C>T

Your query was ambiguous. Multiple possible variants found:

• chrX-113898791-G-A
• chrX-113898791-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000674361.1(XACT):​n.65070C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 109,829 control chromosomes in the GnomAD database, including 11,703 homozygotes. There are 16,681 hemizygotes in GnomAD. 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 0.51 (11703 hom., 16681 hem., cov: 22)
• Consequence: XACT ENST00000674361.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

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.65070C>T		non_coding_transcript_exon_variant	Exon 2 of 2
XACT	ENST00000468762.3	n.293+39402C>T		intron_variant	Intron 3 of 4	5
XACT	ENST00000765932.1	n.359+39402C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.509 AC: 55864 AN: 109781 Hom.: 11707 Cov.: 22

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.530

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.509 AC: 55866 AN: 109829 Hom.: 11703 Cov.: 22 AF XY: 0.519 AC XY: 16681 AN XY: 32113

African (AFR) AF: 0.187 AC: 5650 AN: 30285

American (AMR) AF: 0.516 AC: 5337 AN: 10336

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 1757 AN: 2618

East Asian (EAS) AF: 0.903 AC: 3106 AN: 3441

South Asian (SAS) AF: 0.768 AC: 1902 AN: 2478

European-Finnish (FIN) AF: 0.663 AC: 3798 AN: 5728

Middle Eastern (MID) AF: 0.590 AC: 124 AN: 210

European-Non Finnish (NFE) AF: 0.625 AC: 32862 AN: 52552

Other (OTH) AF: 0.535 AC: 804 AN: 1502

Alfa AF: 0.575 Hom.: 44994

Bravo AF: 0.486

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs2905404; hg19: chrX-113142068;