rs5028798

Variant names:

• chr11-34583888-T-G
• rs5028798

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 0.713 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
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.586 AC: 24320 AN: 41468

American (AMR) AF: 0.669 AC: 10226 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2557 AN: 3470

East Asian (EAS) AF: 0.507 AC: 2623 AN: 5176

South Asian (SAS) AF: 0.710 AC: 3420 AN: 4820

European-Finnish (FIN) AF: 0.782 AC: 8289 AN: 10604

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.802 AC: 54518 AN: 68012

Other (OTH) AF: 0.727 AC: 1539 AN: 2116

Alfa AF: 0.767 Hom.: 193055

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
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs5028798; hg19: chr11-34605435;