rs2467012

Variant names:

• chr12-46061116-A-G
• rs2467012

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 0.413 in 151,810 control chromosomes in the GnomAD database, including 13,389 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 0.41 (13389 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.546 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: 0.413 AC: 62672 AN: 151692 Hom.: 13381 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.413 AC: 62704 AN: 151810 Hom.: 13389 Cov.: 32 AF XY: 0.420 AC XY: 31169 AN XY: 74224

African (AFR) AF: 0.304 AC: 12591 AN: 41452

American (AMR) AF: 0.418 AC: 6369 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1753 AN: 3468

East Asian (EAS) AF: 0.560 AC: 2900 AN: 5176

South Asian (SAS) AF: 0.564 AC: 2720 AN: 4822

European-Finnish (FIN) AF: 0.478 AC: 5014 AN: 10500

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29926 AN: 67834

Other (OTH) AF: 0.403 AC: 848 AN: 2106

Alfa AF: 0.290 Hom.: 744

Bravo AF: 0.402

Asia WGS AF: 0.497 AC: 1726 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.6
DANN	Benign	0.29
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs2467012; hg19: chr12-46454899;