rs2271800

Variant names:

• chr1-59907994-A-C
• rs2271800
• NM_000775.4:c.862-67T>G

Your query was ambiguous. Multiple possible variants found:

• chr1-59907994-A-C
• chr1-59907994-A-T

Variant summary

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

The NM_000775.4(CYP2J2):​c.862-67T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 1,498,338 control chromosomes in the GnomAD database, including 25,736 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 0.24 (5988 hom., cov: 32)
  • Exomes 𝑓: 0.16 (19748 hom.)
• Consequence: CYP2J2 NM_000775.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• Publications: 8 publications found

Genes affected

CYP2J2 (HGNC:2634): (cytochrome P450 family 2 subfamily J member 2) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum and is thought to be the predominant enzyme responsible for epoxidation of endogenous arachidonic acid in cardiac tissue. Multiple transcript variants have been found for this gene. [provided by RefSeq, Jan 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000775.4. 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
	CYP2J2	NM_000775.4	MANE Select	c.862-67T>G		intron	N/A	NP_000766.2
	CYP2J2	NR_134981.2		n.889-67T>G		intron	N/A
	CYP2J2	NR_134982.2		n.889-67T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP2J2	ENST00000371204.4	TSL:1 MANE Select	c.862-67T>G		intron	N/A	ENSP00000360247.3
	CYP2J2	ENST00000466095.5	TSL:3	n.862-67T>G		intron	N/A	ENSP00000498084.1
	CYP2J2	ENST00000468257.2	TSL:3	n.862-67T>G		intron	N/A	ENSP00000497807.1

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36738 AN: 151910 Hom.: 5964 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.0873

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0990

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.193

GnomAD4 exome AF: 0.161 AC: 217121 AN: 1346310 Hom.: 19748 AF XY: 0.158 AC XY: 106186 AN XY: 673568

African (AFR) AF: 0.491 AC: 15126 AN: 30820

American (AMR) AF: 0.156 AC: 6576 AN: 42238

Ashkenazi Jewish (ASJ) AF: 0.0897 AC: 2185 AN: 24372

East Asian (EAS) AF: 0.175 AC: 6808 AN: 38968

South Asian (SAS) AF: 0.0924 AC: 7560 AN: 81824

European-Finnish (FIN) AF: 0.185 AC: 9725 AN: 52652

Middle Eastern (MID) AF: 0.138 AC: 755 AN: 5466

European-Non Finnish (NFE) AF: 0.157 AC: 158743 AN: 1013728

Other (OTH) AF: 0.171 AC: 9643 AN: 56242

GnomAD4 genome AF: 0.242 AC: 36808 AN: 152028 Hom.: 5988 Cov.: 32 AF XY: 0.238 AC XY: 17711 AN XY: 74298

African (AFR) AF: 0.472 AC: 19515 AN: 41388

American (AMR) AF: 0.189 AC: 2891 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0873 AC: 303 AN: 3470

East Asian (EAS) AF: 0.152 AC: 785 AN: 5172

South Asian (SAS) AF: 0.0984 AC: 474 AN: 4816

European-Finnish (FIN) AF: 0.181 AC: 1916 AN: 10596

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10411 AN: 68000

Other (OTH) AF: 0.192 AC: 405 AN: 2108

Alfa AF: 0.166 Hom.: 3353

Bravo AF: 0.252

Asia WGS AF: 0.156 AC: 542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.10
DANN	Benign	0.46
PhyloP100		-2.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2271800; hg19: chr1-60373666; COSMIC: COSV64605643; COSMIC: COSV64605643;