rs5925461

Variant names:

• chrX-150356340-G-A
• rs5925461

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0643 AC: 7201 AN: 112004 Hom.: 176 Cov.: 23

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

African (AFR) AF: 0.0475 AC: 1465 AN: 30854

American (AMR) AF: 0.0534 AC: 566 AN: 10603

Ashkenazi Jewish (ASJ) AF: 0.0502 AC: 133 AN: 2647

East Asian (EAS) AF: 0.0183 AC: 65 AN: 3561

South Asian (SAS) AF: 0.0534 AC: 144 AN: 2695

European-Finnish (FIN) AF: 0.0888 AC: 539 AN: 6073

Middle Eastern (MID) AF: 0.0275 AC: 6 AN: 218

European-Non Finnish (NFE) AF: 0.0781 AC: 4153 AN: 53188

Other (OTH) AF: 0.0659 AC: 101 AN: 1533

Alfa AF: 0.0743 Hom.: 468

Bravo AF: 0.0632

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.70
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs5925461; hg19: chrX-149524594;