rs1474563

Variant names:

• chrX-79393696-C-T
• rs1474563
• ENST00000723698.1:n.224-1114C>T

Variant summary

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

The ENST00000723698.1(ENSG00000294454):​n.224-1114C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 109,788 control chromosomes in the GnomAD database, including 9,376 homozygotes. There are 15,136 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 0.47 (9376 hom., 15136 hem., cov: 22)
• Consequence: ENSG00000294454 ENST00000723698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648
• Publications: 15 publications found

Genes affected

ENSG00000294454 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.574 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
ENSG00000294454	ENST00000723698.1	n.224-1114C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.469 AC: 51503 AN: 109732 Hom.: 9379 Cov.: 22

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.469 AC: 51524 AN: 109788 Hom.: 9376 Cov.: 22 AF XY: 0.472 AC XY: 15136 AN XY: 32086

African (AFR) AF: 0.290 AC: 8796 AN: 30296

American (AMR) AF: 0.401 AC: 4119 AN: 10278

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 1801 AN: 2611

East Asian (EAS) AF: 0.153 AC: 536 AN: 3511

South Asian (SAS) AF: 0.533 AC: 1354 AN: 2540

European-Finnish (FIN) AF: 0.574 AC: 3240 AN: 5646

Middle Eastern (MID) AF: 0.627 AC: 133 AN: 212

European-Non Finnish (NFE) AF: 0.579 AC: 30442 AN: 52540

Other (OTH) AF: 0.505 AC: 754 AN: 1494

Alfa AF: 0.537 Hom.: 70921

Bravo AF: 0.446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.26
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs1474563; hg19: chrX-78649193;