5-28329560-A-G

Variant names:

• chr5-28329560-A-G
• rs1582924

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 0.456 in 151,680 control chromosomes in the GnomAD database, including 16,895 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 0.46 (16895 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.836
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 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: 0.455 AC: 69034 AN: 151562 Hom.: 16862 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.456 AC: 69116 AN: 151680 Hom.: 16895 Cov.: 32 AF XY: 0.459 AC XY: 34047 AN XY: 74122

African (AFR) AF: 0.560 AC: 23218 AN: 41430

American (AMR) AF: 0.556 AC: 8472 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1584 AN: 3466

East Asian (EAS) AF: 0.802 AC: 4121 AN: 5140

South Asian (SAS) AF: 0.519 AC: 2495 AN: 4810

European-Finnish (FIN) AF: 0.351 AC: 3699 AN: 10530

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24194 AN: 67766

Other (OTH) AF: 0.463 AC: 975 AN: 2104

Alfa AF: 0.386 Hom.: 18057

Bravo AF: 0.478

Asia WGS AF: 0.669 AC: 2321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.88
DANN	Benign	0.24
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs1582924; hg19: chr5-28329667;