5-28329560-A-G

Position:

• chr5-28329560-A-G

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 0.456 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.802

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.463

Alfa AF: 0.383 Hom.: 14757

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1582924; hg19: chr5-28329667;