rs2399946

Variant names:

• chrX-746052-A-G
• rs2399946

Your query was ambiguous. Multiple possible variants found:

• chrX-746052-A-G
• chrX-746052-A-T

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 0.272 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41271 AN: 151882 Hom.: 6109 Cov.: 32

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

African (AFR) AF: 0.387 AC: 16023 AN: 41442

American (AMR) AF: 0.185 AC: 2825 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 690 AN: 3466

East Asian (EAS) AF: 0.192 AC: 990 AN: 5168

South Asian (SAS) AF: 0.225 AC: 1082 AN: 4808

European-Finnish (FIN) AF: 0.241 AC: 2544 AN: 10570

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16508 AN: 67938

Other (OTH) AF: 0.240 AC: 507 AN: 2116

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2399946; hg19: chrX-706787;