rs12682834

Variant names:

• chr9-87447908-A-G
• rs12682834

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

GnomAD2 exomes AF: 0.651 AC: 148378 AN: 228042 AF XY: 0.655

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 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

African (AFR) AF: 0.475 AC: 4972 AN: 10462

American (AMR) AF: 0.688 AC: 24848 AN: 36102

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 8534 AN: 11674

East Asian (EAS) AF: 0.686 AC: 9000 AN: 13114

South Asian (SAS) AF: 0.737 AC: 49076 AN: 66578

European-Finnish (FIN) AF: 0.600 AC: 10113 AN: 16868

Middle Eastern (MID) AF: 0.632 AC: 1798 AN: 2844

European-Non Finnish (NFE) AF: 0.630 AC: 120540 AN: 191390

Other (OTH) AF: 0.646 AC: 10689 AN: 16544

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

African (AFR) AF: 0.484 AC: 20061 AN: 41462

American (AMR) AF: 0.642 AC: 9826 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2549 AN: 3470

East Asian (EAS) AF: 0.706 AC: 3638 AN: 5156

South Asian (SAS) AF: 0.747 AC: 3593 AN: 4812

European-Finnish (FIN) AF: 0.583 AC: 6166 AN: 10580

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42762 AN: 67954

Other (OTH) AF: 0.616 AC: 1299 AN: 2110

Alfa AF: 0.631 Hom.: 7131

Bravo AF: 0.595

Asia WGS AF: 0.709 AC: 2462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.38
DANN	Benign	0.28
PhyloP100		-0.56

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12682834;

hg19: chr9-90062823;

COSMIC: COSV60795570;