X-853599-G-A

Variant names:

• chrX-853599-G-A
• rs5946326

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 0.443 in 151,736 control chromosomes in the GnomAD database, including 15,169 homozygotes. There are 32,910 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 0.44 (15169 hom., 32910 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67171 AN: 151618 Hom.: 15143 Cov.: 31

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.443 AC: 67230 AN: 151736 Hom.: 15169 Cov.: 31 AF XY: 0.444 AC XY: 32910 AN XY: 74086

African (AFR) AF: 0.360 AC: 14926 AN: 41408

American (AMR) AF: 0.539 AC: 8206 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1557 AN: 3464

East Asian (EAS) AF: 0.551 AC: 2832 AN: 5140

South Asian (SAS) AF: 0.496 AC: 2375 AN: 4792

European-Finnish (FIN) AF: 0.404 AC: 4252 AN: 10516

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.465 AC: 31563 AN: 67884

Other (OTH) AF: 0.491 AC: 1034 AN: 2106

Bravo AF: 0.452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.67
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs5946326; hg19: chrX-814334;