rs2743467

Variant names:

• chr22-42152889-A-C
• rs2743467

Your query was ambiguous. Multiple possible variants found:

• chr22-42152889-A-C
• chr22-42152889-A-G
• chr22-42152889-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 29)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (Cadd=1.806).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP2D8P		n.42152889A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP2D8P	ENST00000433633.1	n.349+140T>G		intron_variant	Intron 2 of 8	6

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 451776 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 237692

African (AFR) AF: 0.00 AC: 0 AN: 12768

American (AMR) AF: 0.00 AC: 0 AN: 21864

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14106

East Asian (EAS) AF: 0.00 AC: 0 AN: 30910

South Asian (SAS) AF: 0.00 AC: 0 AN: 47560

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29330

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1990

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 267226

Other (OTH) AF: 0.00 AC: 0 AN: 26022

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	1.8
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; hg19: -;