chr2-112933827-A-G

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDK8P2		n.112933827A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;