X-73863786-A-G

Variant names:

• chrX-73863786-A-G
• rs470843

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 0.522 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.521 AC: 57697 AN: 110649 Hom.: 13324 Cov.: 23

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

African (AFR) AF: 0.895 AC: 27182 AN: 30378

American (AMR) AF: 0.408 AC: 4270 AN: 10457

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 852 AN: 2632

East Asian (EAS) AF: 0.943 AC: 3271 AN: 3468

South Asian (SAS) AF: 0.556 AC: 1464 AN: 2633

European-Finnish (FIN) AF: 0.313 AC: 1850 AN: 5908

Middle Eastern (MID) AF: 0.322 AC: 69 AN: 214

European-Non Finnish (NFE) AF: 0.341 AC: 18012 AN: 52817

Other (OTH) AF: 0.437 AC: 664 AN: 1520

Alfa AF: 0.318 Hom.: 2239

Bravo AF: 0.540

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.2
DANN	Benign	0.32
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs470843; hg19: chrX-73083621;