Variant rs12059860 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001099772.2(CYP4B1):c.*437T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0376 in 159,584 control chromosomes in the GnomAD database, including 246 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

Frequency

Genomes: 𝑓 0.039 ( 242 hom., cov: 32)

Exomes 𝑓: 0.017 ( 4 hom. )

Consequence

CYP4B1
NM_001099772.2 3_prime_UTR

Scores

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: 0.622

Variant links:

Genes affected

CYP4B1 (HGNC:2644): (cytochrome P450 family 4 subfamily B member 1) 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. In rodents, the homologous protein has been shown to metabolize certain carcinogens; however, the specific function of the human protein has not been determined. Multiple transcript variants have been found for this gene. [provided by RefSeq, Jan 2016]

CYP4B1 links:

CYP4B1 (HGNC:):

CYP4B1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP4B1	NM_001099772.2 linkuse as main transcript	c.*437T>C		3_prime_UTR_variant	12/12	ENST00000371923.9	NP_001093242.1	P13584-2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
CYP4B1	ENST00000371923.9 linkuse as main transcript	c.*437T>C	3_prime_UTR_variant	12/12	1	NM_001099772.2	ENSP00000360991.4	P13584-2
CYP4B1	ENST00000271153.8 linkuse as main transcript	c.*437T>C	3_prime_UTR_variant	12/12	1		ENSP00000271153.4	P13584-1
CYP4B1	ENST00000464439.6 linkuse as main transcript	n.*925T>C	non_coding_transcript_exon_variant	12/12	3		ENSP00000433068.1	E9PML0
CYP4B1	ENST00000464439.6 linkuse as main transcript	n.*925T>C	3_prime_UTR_variant	12/12	3		ENSP00000433068.1	E9PML0

Frequencies

GnomAD3 genomes

AF:

0.0385

AC:

5864

AN:

152196

Hom.:

239

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0990

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0245

Gnomad ASJ

AF:

0.0228

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0691

Gnomad FIN

AF:

0.00734

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0120

Gnomad OTH

AF:

0.0325

GnomAD4 exome

AF:

0.0166

AC:

121

AN:

7270

Hom.:

Cov.:

AF XY:

0.0180

AC XY:

AN XY:

3722

show subpopulations

Gnomad4 AFR exome

AF:

0.118

Gnomad4 AMR exome

AF:

0.0112

Gnomad4 ASJ exome

AF:

0.0118

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0799

Gnomad4 FIN exome

AF:

0.00980

Gnomad4 NFE exome

AF:

0.0115

Gnomad4 OTH exome

AF:

0.0189

GnomAD4 genome

AF:

0.0386

AC:

5883

AN:

152314

Hom.:

242

Cov.:

AF XY:

0.0382

AC XY:

2849

AN XY:

74490

show subpopulations

Gnomad4 AFR

AF:

0.0991

Gnomad4 AMR

AF:

0.0244

Gnomad4 ASJ

AF:

0.0228

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0694

Gnomad4 FIN

AF:

0.00734

Gnomad4 NFE

AF:

0.0120

Gnomad4 OTH

AF:

0.0321

Alfa

AF:

0.0164

Hom.:

Bravo

AF:

0.0410

Asia WGS

AF:

0.0320

AC:

111

AN:

3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Pulmonary disease, chronic obstructive, susceptibility to

Other:1

association, no assertion criteria provided

research

HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas

Jul 05, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

9.3

DANN

Benign

0.72

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over