rs5925482

Positions:

• chrX-150359692-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 0.0607 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;