rs5925482

Variant names:

• chrX-150359692-A-G
• rs5925482

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 0.0607 in 112,118 control chromosomes in the GnomAD database, including 175 homozygotes. There are 1,937 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 0.061 (175 hom., 1937 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.638

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0761 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: 0.0607 AC: 6804 AN: 112065 Hom.: 174 Cov.: 23 AF XY: 0.0566 AC XY: 1936 AN XY: 34229

Gnomad AFR AF: 0.0353

Gnomad AMI AF: 0.0466

Gnomad AMR AF: 0.0515

Gnomad ASJ AF: 0.0499

Gnomad EAS AF: 0.0196

Gnomad SAS AF: 0.0484

Gnomad FIN AF: 0.0914

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0780

Gnomad OTH AF: 0.0594

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

GnomAD4 genome AF: 0.0607 AC: 6810 AN: 112118 Hom.: 175 Cov.: 23 AF XY: 0.0565 AC XY: 1937 AN XY: 34292

Gnomad4 AFR AF: 0.0353

Gnomad4 AMR AF: 0.0520

Gnomad4 ASJ AF: 0.0499

Gnomad4 EAS AF: 0.0196

Gnomad4 SAS AF: 0.0478

Gnomad4 FIN AF: 0.0914

Gnomad4 NFE AF: 0.0781

Gnomad4 OTH AF: 0.0587

Alfa AF: 0.0719 Hom.: 443

Bravo AF: 0.0591

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5925482; hg19: chrX-149527945;