rs5946328

Variant names:

• chrX-853887-G-A
• rs5946328

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;