rs5946504

Variant names:

• chrX-853815-C-T
• rs5946504

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 0.748 in 151,552 control chromosomes in the GnomAD database, including 43,275 homozygotes. There are 55,593 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 0.75 (43275 hom., 55593 hem., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 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: 0.747 AC: 113196 AN: 151434 Hom.: 43230 Cov.: 29 AF XY: 0.751 AC XY: 55488 AN XY: 73900

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.748 AC: 113296 AN: 151552 Hom.: 43275 Cov.: 29 AF XY: 0.751 AC XY: 55593 AN XY: 74028

Gnomad4 AFR AF: 0.873

Gnomad4 AMR AF: 0.762

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.869

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.730

Bravo AF: 0.760

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5946504; hg19: chrX-814550;