X-746201-A-G

Variant names:

• chrX-746201-A-G
• rs2399945

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 0.135 in 151,986 control chromosomes in the GnomAD database, including 1,541 homozygotes. There are 10,124 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 0.14 (1541 hom., 10124 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20552 AN: 151868 Hom.: 1543 Cov.: 31

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.0887

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.135 AC: 20563 AN: 151986 Hom.: 1541 Cov.: 31 AF XY: 0.136 AC XY: 10124 AN XY: 74272

African (AFR) AF: 0.188 AC: 7798 AN: 41434

American (AMR) AF: 0.0885 AC: 1351 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 421 AN: 3470

East Asian (EAS) AF: 0.186 AC: 960 AN: 5166

South Asian (SAS) AF: 0.182 AC: 873 AN: 4802

European-Finnish (FIN) AF: 0.122 AC: 1292 AN: 10582

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.111 AC: 7526 AN: 67960

Other (OTH) AF: 0.127 AC: 267 AN: 2108

Bravo AF: 0.133

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	4.7
DANN	Benign	0.55
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs2399945; hg19: chrX-706936;