rs4824253

Positions:

• chrX-147836750-A-G

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 0.312 in 110,429 control chromosomes in the GnomAD database, including 4,557 homozygotes. There are 9,695 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 0.31 (4557 hom., 9695 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.312 AC: 34468 AN: 110374 Hom.: 4558 Cov.: 22 AF XY: 0.296 AC XY: 9656 AN XY: 32650

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.00253

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.312 AC: 34508 AN: 110429 Hom.: 4557 Cov.: 22 AF XY: 0.296 AC XY: 9695 AN XY: 32715

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.00254

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.296

Alfa AF: 0.274 Hom.: 14450

Bravo AF: 0.316

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
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: rs4824253; hg19: chrX-146918268;