22-42152889-A-G

Variant names:

• chr22-42152889-A-G
• rs2743467

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 0.372 in 602,228 control chromosomes in the GnomAD database, including 46,729 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 0.45 (17974 hom., cov: 29)
  • Exomes 𝑓: 0.34 (28755 hom.)
• Consequence: CYP2D8P intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.473
• Publications: 10 publications found

Genes affected

CYP2D8P (HGNC:2628): (ccytochrome P450 family 2 subfamily D member 8, pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (Cadd=3.517).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000433633.1. You can select a different transcript below to see updated ACMG assignments.

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
	CYP2D8P	ENST00000433633.1	TSL:6	n.349+140T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68170 AN: 151216 Hom.: 17922 Cov.: 29

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.439

GnomAD4 exome AF: 0.345 AC: 155468 AN: 450894 Hom.: 28755 AF XY: 0.344 AC XY: 81631 AN XY: 237184

African (AFR) AF: 0.747 AC: 9529 AN: 12754

American (AMR) AF: 0.305 AC: 6660 AN: 21810

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 5130 AN: 14086

East Asian (EAS) AF: 0.188 AC: 5793 AN: 30860

South Asian (SAS) AF: 0.362 AC: 17140 AN: 47402

European-Finnish (FIN) AF: 0.391 AC: 11431 AN: 29262

Middle Eastern (MID) AF: 0.407 AC: 807 AN: 1984

European-Non Finnish (NFE) AF: 0.334 AC: 89160 AN: 266768

Other (OTH) AF: 0.378 AC: 9818 AN: 25968

GnomAD4 genome AF: 0.451 AC: 68274 AN: 151334 Hom.: 17974 Cov.: 29 AF XY: 0.449 AC XY: 33186 AN XY: 73908

African (AFR) AF: 0.741 AC: 30567 AN: 41224

American (AMR) AF: 0.354 AC: 5395 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1273 AN: 3460

East Asian (EAS) AF: 0.196 AC: 1000 AN: 5106

South Asian (SAS) AF: 0.372 AC: 1776 AN: 4776

European-Finnish (FIN) AF: 0.409 AC: 4281 AN: 10474

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22667 AN: 67780

Other (OTH) AF: 0.435 AC: 909 AN: 2088

Alfa AF: 0.301 Hom.: 1338

Bravo AF: 0.457

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	3.5
PhyloP100		0.47
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Other links and lift over

dbSNP: rs2743467;