rs5946336

chrX-875373-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;