X-853779-A-G

Variant names:

• chrX-853779-A-G
• rs5946327

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 0.165 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
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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

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

African (AFR) AF: 0.0454 AC: 1881 AN: 41426

American (AMR) AF: 0.210 AC: 3196 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 988 AN: 3462

East Asian (EAS) AF: 0.0670 AC: 342 AN: 5102

South Asian (SAS) AF: 0.150 AC: 715 AN: 4780

European-Finnish (FIN) AF: 0.140 AC: 1472 AN: 10548

Middle Eastern (MID) AF: 0.334 AC: 97 AN: 290

European-Non Finnish (NFE) AF: 0.233 AC: 15826 AN: 67808

Other (OTH) AF: 0.215 AC: 453 AN: 2104

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
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs5946327; hg19: chrX-814514;