rs5946336

Variant names:

• chrX-875373-A-G
• rs5946336

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24846 AN: 151516 Hom.: 3092 Cov.: 30

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

African (AFR) AF: 0.355 AC: 14648 AN: 41318

American (AMR) AF: 0.115 AC: 1758 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.0639 AC: 221 AN: 3460

East Asian (EAS) AF: 0.0675 AC: 347 AN: 5140

South Asian (SAS) AF: 0.103 AC: 496 AN: 4796

European-Finnish (FIN) AF: 0.102 AC: 1065 AN: 10472

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.0877 AC: 5957 AN: 67916

Other (OTH) AF: 0.142 AC: 299 AN: 2100

Bravo AF: 0.173

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.54
DANN	Benign	0.23
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs5946336; hg19: chrX-836108;