rs5925461

chrX-150356340-G-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 0.0643 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;