rs1321391

Positions:

• chrX-115046174-A-G
• chrX-115046174-A-T

Variant summary

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

The variant allele was found at a frequency of 0.525 in 109,882 control chromosomes in the GnomAD database, including 13,077 homozygotes. There are 16,269 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 0.52 (13077 hom., 16269 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.525 AC: 57620 AN: 109827 Hom.: 13080 Cov.: 22 AF XY: 0.505 AC XY: 16219 AN XY: 32127

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.525 AC: 57656 AN: 109882 Hom.: 13077 Cov.: 22 AF XY: 0.505 AC XY: 16269 AN XY: 32192

Gnomad4 AFR AF: 0.880

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.484

Alfa AF: 0.431 Hom.: 22608

Bravo AF: 0.548

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.63
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1321391; hg19: chrX-114280737;