rs3118292

Variant names:

• chr9-25143482-A-G
• rs3118292

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 0.227 in 151,668 control chromosomes in the GnomAD database, including 4,720 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 0.23 (4720 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 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: 0.227 AC: 34435 AN: 151552 Hom.: 4703 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.227 AC: 34489 AN: 151668 Hom.: 4720 Cov.: 32 AF XY: 0.223 AC XY: 16507 AN XY: 74134

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.202

Alfa AF: 0.171 Hom.: 4796

Bravo AF: 0.232

Asia WGS AF: 0.185 AC: 643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3118292; hg19: chr9-25143480;