rs5946336

Variant names:

• chrX-875373-A-G
• rs5946336

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 0.164 in 151,630 control chromosomes in the GnomAD database, including 3,110 homozygotes. There are 12,094 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 0.16 (3110 hom., 12094 hem., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 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: 0.164 AC: 24846 AN: 151516 Hom.: 3092 Cov.: 30 AF XY: 0.163 AC XY: 12041 AN XY: 73938

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0639

Gnomad EAS AF: 0.0675

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.0877

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.164 AC: 24909 AN: 151630 Hom.: 3110 Cov.: 30 AF XY: 0.163 AC XY: 12094 AN XY: 74062

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.0639

Gnomad4 EAS AF: 0.0675

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0877

Gnomad4 OTH AF: 0.142

Bravo AF: 0.173

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.54
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5946336; hg19: chrX-836108;