rs5946533

Variant names:

• chrX-885378-C-T
• rs5946533

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 0.416 in 151,798 control chromosomes in the GnomAD database, including 16,676 homozygotes. There are 31,439 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 0.42 (16676 hom., 31439 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 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: 0.416 AC: 63126 AN: 151680 Hom.: 16633 Cov.: 31 AF XY: 0.423 AC XY: 31329 AN XY: 74034

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.416 AC: 63218 AN: 151798 Hom.: 16676 Cov.: 31 AF XY: 0.424 AC XY: 31439 AN XY: 74162

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.803

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.384

Bravo AF: 0.438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0030
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5946533; hg19: chrX-846113;