rs2399946

Positions:

• chrX-746052-A-G
• chrX-746052-A-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 0.272 in 152,000 control chromosomes in the GnomAD database, including 6,123 homozygotes. There are 19,869 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 0.27 (6123 hom., 19869 hem., cov: 32)
• 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 = 0.382 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: 0.272 AC: 41271 AN: 151882 Hom.: 6109 Cov.: 32 AF XY: 0.267 AC XY: 19814 AN XY: 74154

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.272 AC: 41314 AN: 152000 Hom.: 6123 Cov.: 32 AF XY: 0.267 AC XY: 19869 AN XY: 74282

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.240

Bravo AF: 0.267

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2399946; hg19: chrX-706787;