rs3118516

Variant names:

• chr9-134547946-G-A
• rs3118516

Your query was ambiguous. Multiple possible variants found:

• chr9-134547946-G-A
• chr9-134547946-G-C

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 0.291 in 152,114 control chromosomes in the GnomAD database, including 6,743 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 0.29 (6743 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.75

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.425 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: 0.291 AC: 44238 AN: 151996 Hom.: 6746 Cov.: 33

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.291 AC: 44248 AN: 152114 Hom.: 6743 Cov.: 33 AF XY: 0.289 AC XY: 21456 AN XY: 74328

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.330

Alfa AF: 0.297 Hom.: 1058

Bravo AF: 0.291

Asia WGS AF: 0.305 AC: 1062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.097
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: rs3118516; hg19: chr9-137439792;