rs5946328

Positions:

• chrX-853887-G-A
• chrX-853887-G-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 0.143 in 151,848 control chromosomes in the GnomAD database, including 1,647 homozygotes. There are 10,461 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 0.14 (1647 hom., 10461 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21697 AN: 151728 Hom.: 1650 Cov.: 32 AF XY: 0.141 AC XY: 10442 AN XY: 74058

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.0683

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0655

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0799

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.143 AC: 21708 AN: 151848 Hom.: 1647 Cov.: 32 AF XY: 0.141 AC XY: 10461 AN XY: 74188

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.0657

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.0799

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.142

Bravo AF: 0.152

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.098
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5946328; hg19: chrX-814622;