rs1321391

Variant names:

• chrX-115046174-A-G
• rs1321391

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.525 AC: 57620 AN: 109827 Hom.: 13080 Cov.: 22

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

African (AFR) AF: 0.880 AC: 26493 AN: 30117

American (AMR) AF: 0.420 AC: 4315 AN: 10270

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1186 AN: 2637

East Asian (EAS) AF: 0.157 AC: 543 AN: 3457

South Asian (SAS) AF: 0.478 AC: 1238 AN: 2591

European-Finnish (FIN) AF: 0.341 AC: 1971 AN: 5776

Middle Eastern (MID) AF: 0.457 AC: 96 AN: 210

European-Non Finnish (NFE) AF: 0.397 AC: 20899 AN: 52658

Other (OTH) AF: 0.484 AC: 725 AN: 1497

Alfa AF: 0.460 Hom.: 37562

Bravo AF: 0.548

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.63
DANN	Benign	0.51
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1321391; hg19: chrX-114280737;