9-90793457-A-G

Variant names:

• chr9-90793457-A-G
• rs290258

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 0.181 in 152,020 control chromosomes in the GnomAD database, including 2,747 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 0.18 (2747 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 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: 0.181 AC: 27475 AN: 151902 Hom.: 2750 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.181 AC: 27483 AN: 152020 Hom.: 2747 Cov.: 33 AF XY: 0.184 AC XY: 13705 AN XY: 74316

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.186

Alfa AF: 0.177 Hom.: 1014

Bravo AF: 0.177

Asia WGS AF: 0.302 AC: 1049 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	14
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs290258; hg19: chr9-93555739; COSMIC: COSV53318193;