rs12684950

Variant names:

• chr9-84262016-A-G
• rs12684950

Your query was ambiguous. Multiple possible variants found:

• chr9-84262016-A-G
• chr9-84262016-A-T

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 0.0497 in 152,310 control chromosomes in the GnomAD database, including 461 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 0.050 (461 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 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: 0.0496 AC: 7544 AN: 152190 Hom.: 455 Cov.: 33

Gnomad AFR AF: 0.0871

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0846

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.0837

Gnomad FIN AF: 0.0165

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00800

Gnomad OTH AF: 0.0396

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

GnomAD4 genome AF: 0.0497 AC: 7571 AN: 152310 Hom.: 461 Cov.: 33 AF XY: 0.0526 AC XY: 3918 AN XY: 74482

Gnomad4 AFR AF: 0.0873

Gnomad4 AMR AF: 0.0855

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.0838

Gnomad4 FIN AF: 0.0165

Gnomad4 NFE AF: 0.00798

Gnomad4 OTH AF: 0.0388

Alfa AF: 0.0206 Hom.: 170

Bravo AF: 0.0600

Asia WGS AF: 0.136 AC: 472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	10
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12684950; hg19: chr9-86876931;