rs1263227

Variant names:

• chrX-74256575-G-A
• rs610488
• ENST00000602812.6:n.695+17767C>T

Variant summary

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

The ENST00000602812.6(FTX):​n.695+17767C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0231 in 111,139 control chromosomes in the GnomAD database, including 84 homozygotes. There are 657 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 0.023 (84 hom., 657 hem., cov: 22)
• Consequence: FTX ENST00000602812.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.244
• Publications: 0 publications found

Genes affected

FTX (HGNC:37190): (FTX transcript, XIST regulator) This gene is located upstream of XIST, within the X-inactivation center (XIC). It produces a spliced long non-coding RNA that is thought to positively regulate the expression of XIST, which is essential for the initiation and spread of X-inactivation. [provided by RefSeq, May 2015]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.077 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000602812.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FTX	NR_028379.1		n.695+17767C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FTX	ENST00000602812.6	TSL:1	n.695+17767C>T		intron	N/A
	FTX	ENST00000423992.3	TSL:5	n.870+17767C>T		intron	N/A
	FTX	ENST00000430772.6	TSL:5	n.585+23819C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0231 AC: 2561 AN: 111088 Hom.: 84 Cov.: 22

Gnomad AFR AF: 0.0796

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00867

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000381

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00427

Gnomad NFE AF: 0.000226

Gnomad OTH AF: 0.0225

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

GnomAD4 genome AF: 0.0231 AC: 2568 AN: 111139 Hom.: 84 Cov.: 22 AF XY: 0.0197 AC XY: 657 AN XY: 33395

African (AFR) AF: 0.0796 AC: 2430 AN: 30515

American (AMR) AF: 0.00866 AC: 90 AN: 10388

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2643

East Asian (EAS) AF: 0.00 AC: 0 AN: 3527

South Asian (SAS) AF: 0.000382 AC: 1 AN: 2619

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5930

Middle Eastern (MID) AF: 0.00472 AC: 1 AN: 212

European-Non Finnish (NFE) AF: 0.000226 AC: 12 AN: 53094

Other (OTH) AF: 0.0223 AC: 34 AN: 1528

Alfa AF: 0.0182 Hom.: 50

Bravo AF: 0.0278

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	11
DANN	Benign	0.97
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs610488; hg19: chrX-73476410;