rs5941160

Variant names:

• chrX-89275066-T-G
• rs5941160

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 0.401 in 109,245 control chromosomes in the GnomAD database, including 6,997 homozygotes. There are 12,298 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 0.40 (6997 hom., 12298 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.538

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.496 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

Frequencies

GnomAD3 genomes AF: 0.401 AC: 43779 AN: 109189 Hom.: 7000 Cov.: 21 AF XY: 0.390 AC XY: 12286 AN XY: 31535

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.476

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.401 AC: 43780 AN: 109245 Hom.: 6997 Cov.: 21 AF XY: 0.389 AC XY: 12298 AN XY: 31601

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.432

Alfa AF: 0.440 Hom.: 3456

Bravo AF: 0.389

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5941160; hg19: chrX-88530065;