rs9290781

Variant names:

• chr3-184111945-C-A
• rs9290781

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 0.147 in 150,998 control chromosomes in the GnomAD database, including 1,709 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 0.15 (1709 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.47

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.184 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: 0.147 AC: 22176 AN: 150878 Hom.: 1707 Cov.: 30

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0330

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.147 AC: 22207 AN: 150998 Hom.: 1709 Cov.: 30 AF XY: 0.145 AC XY: 10695 AN XY: 73696

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.0329

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.139

Alfa AF: 0.160 Hom.: 709

Bravo AF: 0.142

Asia WGS AF: 0.141 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.059
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9290781; hg19: chr3-183829733;