rs12682834

chr9-87447908-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;