rs5946331

chrX-854266-A-GchrX-854266-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 0.657 in 151,130 control chromosomes in the GnomAD database, including 33,796 homozygotes. There are 48,688 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 0.66 (33796 hom., 48688 hem., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.907 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: 0.657 AC: 99267 AN: 151010 Hom.: 33760 Cov.: 29 AF XY: 0.659 AC XY: 48593 AN XY: 73698

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.593

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.657 AC: 99362 AN: 151130 Hom.: 33796 Cov.: 29 AF XY: 0.659 AC XY: 48688 AN XY: 73830

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.658

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.929

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.622

Bravo AF: 0.668

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.31
Dann	Benign	0.035

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5946331; hg19: chrX-815001;