rs9290128

Variant names:

• chr3-162592591-A-C
• rs9290128

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 0.174 in 151,798 control chromosomes in the GnomAD database, including 2,664 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 0.17 (2664 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 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: 0.175 AC: 26471 AN: 151680 Hom.: 2663 Cov.: 32

Gnomad AFR AF: 0.0976

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0139

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.174 AC: 26483 AN: 151798 Hom.: 2664 Cov.: 32 AF XY: 0.171 AC XY: 12700 AN XY: 74204

Gnomad4 AFR AF: 0.0976

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.0139

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.163

Alfa AF: 0.221 Hom.: 1837

Bravo AF: 0.163

Asia WGS AF: 0.100 AC: 349 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.1
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9290128; hg19: chr3-162310379;