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rs4646425

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000761.5(CYP1A2):c.832-249C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0233 in 152,274 control chromosomes in the GnomAD database, including 71 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 0.023 ( 71 hom., cov: 32)

Consequence

CYP1A2
NM_000761.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.416
Variant links:
Genes affected
CYP1A2 (HGNC:2596): (cytochrome P450 family 1 subfamily A 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. The protein encoded by this gene localizes to the endoplasmic reticulum and its expression is induced by some polycyclic aromatic hydrocarbons (PAHs), some of which are found in cigarette smoke. The enzyme's endogenous substrate is unknown; however, it is able to metabolize some PAHs to carcinogenic intermediates. Other xenobiotic substrates for this enzyme include caffeine, aflatoxin B1, and acetaminophen. The transcript from this gene contains four Alu sequences flanked by direct repeats in the 3' untranslated region. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0788 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CYP1A2NM_000761.5 linkuse as main transcriptc.832-249C>T intron_variant ENST00000343932.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CYP1A2ENST00000343932.5 linkuse as main transcriptc.832-249C>T intron_variant 1 NM_000761.5 P1

Frequencies

GnomAD3 genomes
AF:
0.0233
AC:
3549
AN:
152156
Hom.:
71
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00432
Gnomad AMI
AF:
0.0230
Gnomad AMR
AF:
0.0274
Gnomad ASJ
AF:
0.0576
Gnomad EAS
AF:
0.0740
Gnomad SAS
AF:
0.0849
Gnomad FIN
AF:
0.0374
Gnomad MID
AF:
0.0570
Gnomad NFE
AF:
0.0215
Gnomad OTH
AF:
0.0278
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0233
AC:
3546
AN:
152274
Hom.:
71
Cov.:
32
AF XY:
0.0261
AC XY:
1943
AN XY:
74440
show subpopulations
Gnomad4 AFR
AF:
0.00431
Gnomad4 AMR
AF:
0.0273
Gnomad4 ASJ
AF:
0.0576
Gnomad4 EAS
AF:
0.0734
Gnomad4 SAS
AF:
0.0856
Gnomad4 FIN
AF:
0.0374
Gnomad4 NFE
AF:
0.0215
Gnomad4 OTH
AF:
0.0275
Alfa
AF:
0.0240
Hom.:
78
Bravo
AF:
0.0201
Asia WGS
AF:
0.0660
AC:
229
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
Cadd
Benign
4.8
Dann
Benign
0.50

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: rs4646425; hg19: chr15-75043281; API