chrX-73863786-A-G

Position:

• chrX-73863786-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 0.522 in 110,698 control chromosomes in the GnomAD database, including 13,331 homozygotes. There are 16,971 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 0.52 (13331 hom., 16971 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.521 AC: 57697 AN: 110649 Hom.: 13324 Cov.: 23 AF XY: 0.515 AC XY: 16929 AN XY: 32863

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.522 AC: 57751 AN: 110698 Hom.: 13331 Cov.: 23 AF XY: 0.515 AC XY: 16971 AN XY: 32922

Gnomad4 AFR AF: 0.895

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.437

Alfa AF: 0.318 Hom.: 2239

Bravo AF: 0.540

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.2
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs470843; hg19: chrX-73083621;