rs500428

Variant names:

• chr9-133279770-G-A
• rs500428

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 0.26 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.259 AC: 10757 AN: 41508

American (AMR) AF: 0.381 AC: 5811 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 958 AN: 3470

East Asian (EAS) AF: 0.293 AC: 1516 AN: 5168

South Asian (SAS) AF: 0.215 AC: 1039 AN: 4822

European-Finnish (FIN) AF: 0.195 AC: 2066 AN: 10578

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16650 AN: 68010

Other (OTH) AF: 0.256 AC: 542 AN: 2116

Alfa AF: 0.267 Hom.: 894

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
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs500428; hg19: chr9-136155343;