rs290278

Variant names:

• chr9-90762564-A-G
• rs290278

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 0.936 in 152,118 control chromosomes in the GnomAD database, including 66,787 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 0.94 (66787 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.936 AC: 142297 AN: 152000 Hom.: 66734 Cov.: 30

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.955

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.956

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.945

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

GnomAD4 genome AF: 0.936 AC: 142410 AN: 152118 Hom.: 66787 Cov.: 30 AF XY: 0.938 AC XY: 69704 AN XY: 74342

Gnomad4 AFR AF: 0.980

Gnomad4 AMR AF: 0.955

Gnomad4 ASJ AF: 0.917

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.957

Gnomad4 FIN AF: 0.908

Gnomad4 NFE AF: 0.905

Gnomad4 OTH AF: 0.946

Alfa AF: 0.917 Hom.: 7946

Bravo AF: 0.942

Asia WGS AF: 0.979 AC: 3405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.50
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs290278; hg19: chr9-93524846;