rs5928719

Variant names:

• chrX-35047456-G-A
• rs5928719

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 0.179 in 111,139 control chromosomes in the GnomAD database, including 1,293 homozygotes. There are 5,660 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 0.18 (1293 hom., 5660 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.464

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 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: 0.179 AC: 19917 AN: 111086 Hom.: 1294 Cov.: 22 AF XY: 0.169 AC XY: 5641 AN XY: 33332

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.179 AC: 19927 AN: 111139 Hom.: 1293 Cov.: 22 AF XY: 0.169 AC XY: 5660 AN XY: 33395

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.150

Alfa AF: 0.175 Hom.: 2615

Bravo AF: 0.184

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5928719; hg19: chrX-35065573;