chr5-25928457-G-A

Variant names:

• chr5-25928457-G-A
• rs6873221

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 0.467 in 151,678 control chromosomes in the GnomAD database, including 16,688 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 0.47 (16688 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354

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 (EAS) allele frequency at 95% confidence interval = 0.576 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: 0.467 AC: 70722 AN: 151558 Hom.: 16673 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.428

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.467 AC: 70781 AN: 151678 Hom.: 16688 Cov.: 32 AF XY: 0.468 AC XY: 34704 AN XY: 74114

Gnomad4 AFR AF: 0.521

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.448

Alfa AF: 0.453 Hom.: 2528

Bravo AF: 0.466

Asia WGS AF: 0.554 AC: 1904 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6873221; hg19: chr5-25928566;