X-853779-A-G

Variant names:

• chrX-853779-A-G
• rs5946327

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 0.165 in 151,628 control chromosomes in the GnomAD database, including 2,629 homozygotes. There are 11,931 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 0.17 (2629 hom., 11931 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25090 AN: 151512 Hom.: 2632 Cov.: 31 AF XY: 0.161 AC XY: 11930 AN XY: 73934

Gnomad AFR AF: 0.0456

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.0669

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.346

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.165 AC: 25075 AN: 151628 Hom.: 2629 Cov.: 31 AF XY: 0.161 AC XY: 11931 AN XY: 74062

Gnomad4 AFR AF: 0.0454

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.0670

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.215

Bravo AF: 0.168

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5946327; hg19: chrX-814514;