chrX-20765081-A-G

Position:

• chrX-20765081-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 0.0697 in 111,350 control chromosomes in the GnomAD database, including 332 homozygotes. There are 2,066 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 0.070 (332 hom., 2066 hem., cov: 23)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.20765081A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0697 AC: 7757 AN: 111298 Hom.: 333 Cov.: 23 AF XY: 0.0614 AC XY: 2058 AN XY: 33536

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.0839

Gnomad AMR AF: 0.0482

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.0139

Gnomad SAS AF: 0.0109

Gnomad FIN AF: 0.0193

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0360

Gnomad OTH AF: 0.0628

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

GnomAD4 genome AF: 0.0697 AC: 7760 AN: 111350 Hom.: 332 Cov.: 23 AF XY: 0.0615 AC XY: 2066 AN XY: 33598

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.0482

Gnomad4 ASJ AF: 0.0444

Gnomad4 EAS AF: 0.0139

Gnomad4 SAS AF: 0.0110

Gnomad4 FIN AF: 0.0193

Gnomad4 NFE AF: 0.0360

Gnomad4 OTH AF: 0.0627

Alfa AF: 0.0457 Hom.: 1405

Bravo AF: 0.0794

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.95
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521918; hg19: chrX-20783199;