rs5932755

chrX-125806388-T-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 0.26 in 108,626 control chromosomes in the GnomAD database, including 2,976 homozygotes. There are 7,760 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 0.26 (2976 hom., 7760 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.325 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: 0.260 AC: 28227 AN: 108586 Hom.: 2976 Cov.: 21 AF XY: 0.249 AC XY: 7756 AN XY: 31110

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.0430

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.300

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.260 AC: 28220 AN: 108626 Hom.: 2976 Cov.: 21 AF XY: 0.249 AC XY: 7760 AN XY: 31160

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.0432

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.272

Alfa AF: 0.283 Hom.: 1788

Bravo AF: 0.250

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.028
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5932755; hg19: chrX-124940370;