rs12682834

Variant names:

• chr9-87447908-A-G
• rs12682834

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 0.638 in 517,622 control chromosomes in the GnomAD database, including 107,041 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 0.60 (27523 hom., cov: 32)
  • Exomes 𝑓: 0.66 (79518 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.726 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: 0.596 AC: 90593 AN: 151926 Hom.: 27499 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.614

GnomAD3 exomes AF: 0.651 AC: 148378 AN: 228042 Hom.: 48885 AF XY: 0.655 AC XY: 82611 AN XY: 126058

Gnomad AFR exome AF: 0.472

Gnomad AMR exome AF: 0.689

Gnomad ASJ exome AF: 0.733

Gnomad EAS exome AF: 0.685

Gnomad SAS exome AF: 0.740

Gnomad FIN exome AF: 0.591

Gnomad NFE exome AF: 0.629

Gnomad OTH exome AF: 0.655

GnomAD4 exome AF: 0.655 AC: 239570 AN: 365576 Hom.: 79518 Cov.: 0 AF XY: 0.664 AC XY: 139197 AN XY: 209704

Gnomad4 AFR exome AF: 0.475

Gnomad4 AMR exome AF: 0.688

Gnomad4 ASJ exome AF: 0.731

Gnomad4 EAS exome AF: 0.686

Gnomad4 SAS exome AF: 0.737

Gnomad4 FIN exome AF: 0.600

Gnomad4 NFE exome AF: 0.630

Gnomad4 OTH exome AF: 0.646

GnomAD4 genome AF: 0.596 AC: 90643 AN: 152046 Hom.: 27523 Cov.: 32 AF XY: 0.596 AC XY: 44295 AN XY: 74324

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.706

Gnomad4 SAS AF: 0.747

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.616

Alfa AF: 0.634 Hom.: 7025

Bravo AF: 0.595

Asia WGS AF: 0.709 AC: 2462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.38
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12682834; hg19: chr9-90062823; COSMIC: COSV60795570;