rs521362

Positions:

• chrX-67018503-C-T

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/exons	MANE	UniProt

Ensembl

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