rs12467847

Variant names:

• chr2-112933827-A-G
• rs12467847

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 0.391 in 152,082 control chromosomes in the GnomAD database, including 12,079 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 0.39 (12079 hom., cov: 33)
• Consequence: CDK8P2 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.12
• Publications: 4 publications found

Genes affected

CDK8P2 (HGNC:52296): (cyclin dependent kinase 8 pseudogene 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.476 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: 0.391 AC: 59436 AN: 151964 Hom.: 12058 Cov.: 33

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.391 AC: 59499 AN: 152082 Hom.: 12079 Cov.: 33 AF XY: 0.394 AC XY: 29312 AN XY: 74322

African (AFR) AF: 0.477 AC: 19781 AN: 41458

American (AMR) AF: 0.485 AC: 7416 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1048 AN: 3468

East Asian (EAS) AF: 0.299 AC: 1546 AN: 5176

South Asian (SAS) AF: 0.380 AC: 1833 AN: 4820

European-Finnish (FIN) AF: 0.359 AC: 3795 AN: 10566

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.337 AC: 22905 AN: 68002

Other (OTH) AF: 0.373 AC: 787 AN: 2108

Alfa AF: 0.385 Hom.: 10348

Bravo AF: 0.406

Asia WGS AF: 0.354 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	12
DANN	Benign	0.66
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs12467847; hg19: chr2-113691404; COSMIC: COSV69293184;