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rs762551

Variant summary

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

The NM_000761.5(CYP1A2):c.-9-154C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 152,062 control chromosomes in the GnomAD database, including 34,665 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.67 ( 34665 hom., cov: 32)

Consequence

CYP1A2
NM_000761.5 intron

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.24
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=-0.95).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CYP1A2NM_000761.5 linkuse as main transcriptc.-9-154C>A intron_variant ENST00000343932.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CYP1A2ENST00000343932.5 linkuse as main transcriptc.-9-154C>A intron_variant 1 NM_000761.5 P1

Frequencies

GnomAD3 genomes
AF:
0.672
AC:
102144
AN:
151944
Hom.:
34631
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.605
Gnomad AMI
AF:
0.650
Gnomad AMR
AF:
0.706
Gnomad ASJ
AF:
0.686
Gnomad EAS
AF:
0.651
Gnomad SAS
AF:
0.567
Gnomad FIN
AF:
0.689
Gnomad MID
AF:
0.668
Gnomad NFE
AF:
0.712
Gnomad OTH
AF:
0.666
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.672
AC:
102235
AN:
152062
Hom.:
34665
Cov.:
32
AF XY:
0.668
AC XY:
49693
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.605
Gnomad4 AMR
AF:
0.706
Gnomad4 ASJ
AF:
0.686
Gnomad4 EAS
AF:
0.651
Gnomad4 SAS
AF:
0.568
Gnomad4 FIN
AF:
0.689
Gnomad4 NFE
AF:
0.712
Gnomad4 OTH
AF:
0.667
Alfa
AF:
0.681
Hom.:
16123
Bravo
AF:
0.676
Asia WGS
AF:
0.661
AC:
2300
AN:
3478

ClinVar

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

Submissions by phenotype

not specified Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxMar 09, 2018This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
Cadd
Benign
0.0070
Dann
Benign
0.69

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: rs762551; hg19: chr15-75041917; COSMIC: COSV59659144; API