rs28899

Variant names:

• chr5-83467264-A-G
• rs28899

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 0.479 in 152,046 control chromosomes in the GnomAD database, including 20,857 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 0.48 (20857 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 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: 0.479 AC: 72736 AN: 151928 Hom.: 20820 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.479 AC: 72827 AN: 152046 Hom.: 20857 Cov.: 32 AF XY: 0.481 AC XY: 35728 AN XY: 74320

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.450

Alfa AF: 0.391 Hom.: 1797

Bravo AF: 0.503

Asia WGS AF: 0.513 AC: 1782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.39
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: rs28899; hg19: chr5-82763083;