Variant 2-72132183-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_019885.4(CYP26B1):c.*44T>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 0.167 in 1,569,968 control chromosomes in the GnomAD database, including 24,039 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 3726 hom., cov: 33)

Exomes 𝑓: 0.16 ( 20313 hom. )

Consequence

CYP26B1
NM_019885.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.933

Variant links:

Genes affected

CYP26B1 (HGNC:20581): (cytochrome P450 family 26 subfamily B member 1) This gene encodes a member of the cytochrome P450 superfamily. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. The encoded protein is localized to the endoplasmic reticulum, and functions as a critical regulator of all-trans retinoic acid levels by the specific inactivation of all-trans retinoic acid to hydroxylated forms. Mutations in this gene are associated with radiohumeral fusions and other skeletal and craniofacial anomalies, and increased levels of the encoded protein are associated with atherosclerotic lesions. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2013]

CYP26B1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 2-72132183-A-G is Benign according to our data. Variant chr2-72132183-A-G is described in ClinVar as [Benign]. Clinvar id is 1235982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP26B1	NM_019885.4 linkuse as main transcript	c.*44T>C		3_prime_UTR_variant	6/6	ENST00000001146.7	NP_063938.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP26B1	ENST00000001146.7 linkuse as main transcript	c.*44T>C	3_prime_UTR_variant	6/6	1	NM_019885.4	ENSP00000001146	P1	Q9NR63-1
CYP26B1	ENST00000412253.1 linkuse as main transcript	c.*44T>C	3_prime_UTR_variant	5/5	1		ENSP00000401465
CYP26B1	ENST00000546307.5 linkuse as main transcript	c.*44T>C	3_prime_UTR_variant	5/5	1		ENSP00000443304		Q9NR63-2

Frequencies

GnomAD3 genomes

AF:

0.203

AC:

30829

AN:

151984

Hom.:

3704

Cov.:

show subpopulations

Gnomad AFR

AF:

0.330

Gnomad AMI

AF:

0.0604

Gnomad AMR

AF:

0.222

Gnomad ASJ

AF:

0.125

Gnomad EAS

AF:

0.0781

Gnomad SAS

AF:

0.105

Gnomad FIN

AF:

0.142

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.154

Gnomad OTH

AF:

0.183

GnomAD3 exomes

AF:

0.171

AC:

31800

AN:

185526

Hom.:

3353

AF XY:

0.162

AC XY:

16090

AN XY:

99292

show subpopulations

Gnomad AFR exome

AF:

0.329

Gnomad AMR exome

AF:

0.310

Gnomad ASJ exome

AF:

0.128

Gnomad EAS exome

AF:

0.0719

Gnomad SAS exome

AF:

0.103

Gnomad FIN exome

AF:

0.144

Gnomad NFE exome

AF:

0.152

Gnomad OTH exome

AF:

0.167

GnomAD4 exome

AF:

0.163

AC:

230655

AN:

1417866

Hom.:

20313

Cov.:

AF XY:

0.159

AC XY:

111617

AN XY:

701250

show subpopulations

Gnomad4 AFR exome

AF:

0.328

Gnomad4 AMR exome

AF:

0.299

Gnomad4 ASJ exome

AF:

0.125

Gnomad4 EAS exome

AF:

0.0786

Gnomad4 SAS exome

AF:

0.104

Gnomad4 FIN exome

AF:

0.141

Gnomad4 NFE exome

AF:

0.162

Gnomad4 OTH exome

AF:

0.164

GnomAD4 genome

AF:

0.203

AC:

30893

AN:

152102

Hom.:

3726

Cov.:

AF XY:

0.200

AC XY:

14861

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.330

Gnomad4 AMR

AF:

0.221

Gnomad4 ASJ

AF:

0.125

Gnomad4 EAS

AF:

0.0779

Gnomad4 SAS

AF:

0.103

Gnomad4 FIN

AF:

0.142

Gnomad4 NFE

AF:

0.154

Gnomad4 OTH

AF:

0.188

Alfa

AF:

0.165

Hom.:

448

Bravo

AF:

0.218

Asia WGS

AF:

0.131

AC:

459

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 08, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

8.0

DANN

Benign

0.34

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