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GeneBe

1-59916002-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_000775.4(CYP2J2):c.309C>T(p.His103=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00299 in 1,614,016 control chromosomes in the GnomAD database, including 143 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.016 ( 78 hom., cov: 32)
Exomes 𝑓: 0.0016 ( 65 hom. )

Consequence

CYP2J2
NM_000775.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.85
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-59916002-G-A is Benign according to our data. Variant chr1-59916002-G-A is described in ClinVar as [Benign]. Clinvar id is 791796.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.86 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0544 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CYP2J2NM_000775.4 linkuse as main transcriptc.309C>T p.His103= synonymous_variant 2/9 ENST00000371204.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CYP2J2ENST00000371204.4 linkuse as main transcriptc.309C>T p.His103= synonymous_variant 2/91 NM_000775.4 P1
CYP2J2ENST00000468257.2 linkuse as main transcriptc.309C>T p.His103= synonymous_variant, NMD_transcript_variant 2/103
CYP2J2ENST00000466095.5 linkuse as main transcriptc.309C>T p.His103= synonymous_variant, NMD_transcript_variant 2/83
CYP2J2ENST00000469406.6 linkuse as main transcriptc.*70C>T 3_prime_UTR_variant, NMD_transcript_variant 2/103

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0160
AC:
2441
AN:
152166
Hom.:
78
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0563
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00478
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000118
Gnomad OTH
AF:
0.0110
GnomAD3 exomes
AF:
0.00410
AC:
1031
AN:
251368
Hom.:
24
AF XY:
0.00305
AC XY:
414
AN XY:
135850
show subpopulations
Gnomad AFR exome
AF:
0.0580
Gnomad AMR exome
AF:
0.00208
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000792
Gnomad OTH exome
AF:
0.00114
GnomAD4 exome
AF:
0.00163
AC:
2379
AN:
1461732
Hom.:
65
Cov.:
31
AF XY:
0.00142
AC XY:
1035
AN XY:
727176
show subpopulations
Gnomad4 AFR exome
AF:
0.0596
Gnomad4 AMR exome
AF:
0.00230
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000928
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000405
Gnomad4 OTH exome
AF:
0.00361
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0161
AC:
2449
AN:
152284
Hom.:
78
Cov.:
32
AF XY:
0.0153
AC XY:
1143
AN XY:
74466
show subpopulations
Gnomad4 AFR
AF:
0.0563
Gnomad4 AMR
AF:
0.00477
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000118
Gnomad4 OTH
AF:
0.0109
Alfa
AF:
0.00357
Hom.:
14
Bravo
AF:
0.0186
Asia WGS
AF:
0.00231
AC:
8
AN:
3478
EpiCase
AF:
0.0000545
EpiControl
AF:
0.0000593

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeMar 29, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
Cadd
Benign
2.8
Dann
Benign
0.32

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2229190; hg19: chr1-60381674; API