rs500428

Variant names:

• chr9-133279770-G-A
• rs500428

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 0.26 in 152,148 control chromosomes in the GnomAD database, including 5,386 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 0.26 (5386 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.372 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: 0.260 AC: 39470 AN: 152030 Hom.: 5381 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.260 AC: 39497 AN: 152148 Hom.: 5386 Cov.: 32 AF XY: 0.260 AC XY: 19337 AN XY: 74394

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.256

Alfa AF: 0.268 Hom.: 624

Bravo AF: 0.278

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs500428; hg19: chr9-136155343;