rs5952066

Positions:

• chrX-147803630-C-A

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 0.23 in 110,632 control chromosomes in the GnomAD database, including 2,710 homozygotes. There are 7,089 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 0.23 (2710 hom., 7089 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.309

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 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: 0.230 AC: 25405 AN: 110576 Hom.: 2709 Cov.: 23 AF XY: 0.215 AC XY: 7051 AN XY: 32836

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.0539

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.00169

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.230 AC: 25444 AN: 110632 Hom.: 2710 Cov.: 23 AF XY: 0.215 AC XY: 7089 AN XY: 32902

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.00170

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.229

Alfa AF: 0.198 Hom.: 8195

Bravo AF: 0.237

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5952066; hg19: chrX-146885148;