rs5925461

Variant names:

• chrX-150356340-G-A
• rs5925461

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 0.0643 in 112,059 control chromosomes in the GnomAD database, including 177 homozygotes. There are 2,017 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 0.064 (177 hom., 2017 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• 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: 0.0643 AC: 7201 AN: 112004 Hom.: 176 Cov.: 23 AF XY: 0.0590 AC XY: 2016 AN XY: 34154

Gnomad AFR AF: 0.0476

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.0529

Gnomad ASJ AF: 0.0502

Gnomad EAS AF: 0.0182

Gnomad SAS AF: 0.0536

Gnomad FIN AF: 0.0888

Gnomad MID AF: 0.0251

Gnomad NFE AF: 0.0781

Gnomad OTH AF: 0.0667

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

GnomAD4 genome AF: 0.0643 AC: 7206 AN: 112059 Hom.: 177 Cov.: 23 AF XY: 0.0589 AC XY: 2017 AN XY: 34219

Gnomad4 AFR AF: 0.0475

Gnomad4 AMR AF: 0.0534

Gnomad4 ASJ AF: 0.0502

Gnomad4 EAS AF: 0.0183

Gnomad4 SAS AF: 0.0534

Gnomad4 FIN AF: 0.0888

Gnomad4 NFE AF: 0.0781

Gnomad4 OTH AF: 0.0659

Alfa AF: 0.0743 Hom.: 468

Bravo AF: 0.0632

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5925461; hg19: chrX-149524594;