X-746201-A-G

Position:

• chrX-746201-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 0.135 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.746201A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20552 AN: 151868 Hom.: 1543 Cov.: 31 AF XY: 0.136 AC XY: 10103 AN XY: 74144

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

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.0885

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.127

Bravo AF: 0.133

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2399945; hg19: chrX-706936;