rs1458583

Variant names:

• chrX-128170894-A-T
• rs1458583
• ENST00000660383.1:n.1169-55050T>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000660383.1(ENSG00000225689):​n.1169-55050T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 110,583 control chromosomes in the GnomAD database, including 1,461 homozygotes. There are 5,904 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 0.18 (1461 hom., 5904 hem., cov: 22)
• Consequence: ENSG00000225689 ENST00000660383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763

Genes affected

ENSG00000225689 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.266 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
ENSG00000225689	ENST00000660383.1	n.1169-55050T>A		intron_variant	Intron 9 of 10

Frequencies

GnomAD3 genomes AF: 0.181 AC: 20052 AN: 110530 Hom.: 1458 Cov.: 22 AF XY: 0.179 AC XY: 5873 AN XY: 32868

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.0763

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.132

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.182 AC: 20089 AN: 110583 Hom.: 1461 Cov.: 22 AF XY: 0.179 AC XY: 5904 AN XY: 32931

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.0763

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.181

Alfa AF: 0.165 Hom.: 915

Bravo AF: 0.197

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.94
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1458583; hg19: chrX-127304871;