rs5028798

Variant names:

• chr11-34583888-T-G
• rs5028798

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 0.713 in 152,154 control chromosomes in the GnomAD database, including 39,527 homozygotes. 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 0.71 (39527 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.796 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: 0.713 AC: 108456 AN: 152036 Hom.: 39507 Cov.: 33

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.713 AC: 108526 AN: 152154 Hom.: 39527 Cov.: 33 AF XY: 0.711 AC XY: 52859 AN XY: 74382

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.802

Gnomad4 OTH AF: 0.727

Alfa AF: 0.776 Hom.: 90419

Bravo AF: 0.698

Asia WGS AF: 0.601 AC: 2091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5028798; hg19: chr11-34605435;