22-42149230-G-A

Variant names:

• chr22-42149230-G-A
• rs5751229
• ENST00000651010.1:n.177+49C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651010.1(CYP2D7):​n.177+49C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,190 control chromosomes in the GnomAD database, including 3,679 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 0.21 (3679 hom., cov: 32)
• Consequence: CYP2D7 ENST00000651010.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108
• Publications: 17 publications found

Genes affected

CYP2D7 (HGNC:2624): (cytochrome P450 family 2 subfamily D member 7 (gene/pseudogene)) This gene is a member of the cytochrome P450 gene superfamily. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This gene is a segregating pseudogene, where some individuals may have an allele that encodes a functional enzyme, while other individuals have an allele encoding a protein that is predicted to be non-functional. In this case, the functional allele is thought to be rare. This locus is part of a cluster of cytochrome P450 genes on chromosome 22. [provided by RefSeq, Jan 2017]

LOC105377203 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651010.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP2D7	ENST00000651010.1		n.177+49C>T		intron	N/A
	CYP2D7	ENST00000711577.1		n.222+49C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32595 AN: 152072 Hom.: 3677 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.214 AC: 32599 AN: 152190 Hom.: 3679 Cov.: 32 AF XY: 0.209 AC XY: 15525 AN XY: 74396

African (AFR) AF: 0.218 AC: 9049 AN: 41490

American (AMR) AF: 0.161 AC: 2463 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 876 AN: 3470

East Asian (EAS) AF: 0.407 AC: 2106 AN: 5176

South Asian (SAS) AF: 0.154 AC: 744 AN: 4828

European-Finnish (FIN) AF: 0.127 AC: 1342 AN: 10608

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15308 AN: 68004

Other (OTH) AF: 0.191 AC: 402 AN: 2108

Alfa AF: 0.212 Hom.: 701

Bravo AF: 0.217

Asia WGS AF: 0.250 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.29
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs5751229; hg19: chr22-42545221;