rs5925482

Variant names:

• chrX-150359692-A-G
• rs5925482

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 0.0607 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• 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: 0.0607 AC: 6804 AN: 112065 Hom.: 174 Cov.: 23

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

African (AFR) AF: 0.0353 AC: 1090 AN: 30863

American (AMR) AF: 0.0520 AC: 555 AN: 10666

Ashkenazi Jewish (ASJ) AF: 0.0499 AC: 132 AN: 2643

East Asian (EAS) AF: 0.0196 AC: 70 AN: 3565

South Asian (SAS) AF: 0.0478 AC: 129 AN: 2696

European-Finnish (FIN) AF: 0.0914 AC: 557 AN: 6092

Middle Eastern (MID) AF: 0.0278 AC: 6 AN: 216

European-Non Finnish (NFE) AF: 0.0781 AC: 4149 AN: 53157

Other (OTH) AF: 0.0587 AC: 90 AN: 1534

Alfa AF: 0.0719 Hom.: 443

Bravo AF: 0.0591

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.80
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs5925482; hg19: chrX-149527945;