rs521362

Variant names:

• chrX-67018503-C-T
• rs521362

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 0.337 in 110,313 control chromosomes in the GnomAD database, including 8,588 homozygotes. There are 10,248 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 0.34 (8588 hom., 10248 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.834 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: 0.337 AC: 37149 AN: 110264 Hom.: 8577 Cov.: 22 AF XY: 0.313 AC XY: 10202 AN XY: 32572

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.0797

Gnomad EAS AF: 0.00142

Gnomad SAS AF: 0.0767

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.337 AC: 37210 AN: 110313 Hom.: 8588 Cov.: 22 AF XY: 0.314 AC XY: 10248 AN XY: 32631

Gnomad4 AFR AF: 0.843

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.0797

Gnomad4 EAS AF: 0.00143

Gnomad4 SAS AF: 0.0767

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.289

Alfa AF: 0.214 Hom.: 2358

Bravo AF: 0.359

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs521362; hg19: chrX-66238345;