rs28899

Variant names:

• chr5-83467264-A-G
• rs28899

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 0.479 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.804 AC: 33354 AN: 41472

American (AMR) AF: 0.456 AC: 6963 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1575 AN: 3472

East Asian (EAS) AF: 0.484 AC: 2496 AN: 5162

South Asian (SAS) AF: 0.482 AC: 2314 AN: 4804

European-Finnish (FIN) AF: 0.331 AC: 3504 AN: 10576

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.312 AC: 21178 AN: 67962

Other (OTH) AF: 0.450 AC: 950 AN: 2112

Alfa AF: 0.407 Hom.: 2044

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs28899; hg19: chr5-82763083;