Variant rs3833221 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_000774.5(CYP2F1):c.15dup(p.Thr6HisfsTer22) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 1,613,132 control chromosomes in the GnomAD database, including 36,556 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.26 ( 5591 hom., cov: 22)

Exomes 𝑓: 0.20 ( 30965 hom. )

Consequence

CYP2F1
NM_000774.5 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0400

Variant links:

Genes affected

CYP2F1 (HGNC:2632): (cytochrome P450 family 2 subfamily F 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 and is known to dehydrogenate 3-methylindole, an endogenous toxin derived from the fermentation of tryptophan, as well as xenobiotic substrates such as naphthalene and ethoxycoumarin. This gene is part of a large cluster of cytochrome P450 genes from the CYP2A, CYP2B and CYP2F subfamilies on chromosome 19q. [provided by RefSeq, Jul 2008]

CYP2F1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 19-41116202-G-GC is Benign according to our data. Variant chr19-41116202-G-GC is described in ClinVar as [Benign]. Clinvar id is 402583.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP2F1	NM_000774.5 linkuse as main transcript	c.15dup	p.Thr6HisfsTer22	frameshift_variant	2/10	ENST00000331105.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP2F1	ENST00000331105.7 linkuse as main transcript	c.15dup	p.Thr6HisfsTer22	frameshift_variant	2/10	1	NM_000774.5	P1	P24903-1
CYP2F1	ENST00000532164.2 linkuse as main transcript	c.15dup	p.Thr6HisfsTer22	frameshift_variant, NMD_transcript_variant	2/10	1			P24903-2
CYP2F1	ENST00000531409.5 linkuse as main transcript	n.90dup		non_coding_transcript_exon_variant	2/8	2
CYP2F1	ENST00000526093.5 linkuse as main transcript	n.62-252dup		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes

AF:

0.255

AC:

38741

AN:

151644

Hom.:

5576

Cov.:

show subpopulations

Gnomad AFR

AF:

0.400

Gnomad AMI

AF:

0.288

Gnomad AMR

AF:

0.191

Gnomad ASJ

AF:

0.167

Gnomad EAS

AF:

0.254

Gnomad SAS

AF:

0.242

Gnomad FIN

AF:

0.233

Gnomad MID

AF:

0.222

Gnomad NFE

AF:

0.192

Gnomad OTH

AF:

0.231

GnomAD3 exomes

AF:

0.208

AC:

52137

AN:

250814

Hom.:

6000

AF XY:

0.208

AC XY:

28151

AN XY:

135544

show subpopulations

Gnomad AFR exome

AF:

0.398

Gnomad AMR exome

AF:

0.138

Gnomad ASJ exome

AF:

0.166

Gnomad EAS exome

AF:

0.249

Gnomad SAS exome

AF:

0.227

Gnomad FIN exome

AF:

0.244

Gnomad NFE exome

AF:

0.188

Gnomad OTH exome

AF:

0.191

GnomAD4 exome

AF:

0.201

AC:

293358

AN:

1461370

Hom.:

30965

Cov.:

AF XY:

0.201

AC XY:

146254

AN XY:

726984

show subpopulations

Gnomad4 AFR exome

AF:

0.406

Gnomad4 AMR exome

AF:

0.142

Gnomad4 ASJ exome

AF:

0.168

Gnomad4 EAS exome

AF:

0.237

Gnomad4 SAS exome

AF:

0.225

Gnomad4 FIN exome

AF:

0.238

Gnomad4 NFE exome

AF:

0.192

Gnomad4 OTH exome

AF:

0.211

GnomAD4 genome

AF:

0.256

AC:

38807

AN:

151762

Hom.:

5591

Cov.:

AF XY:

0.255

AC XY:

18896

AN XY:

74156

show subpopulations

Gnomad4 AFR

AF:

0.400

Gnomad4 AMR

AF:

0.191

Gnomad4 ASJ

AF:

0.167

Gnomad4 EAS

AF:

0.254

Gnomad4 SAS

AF:

0.243

Gnomad4 FIN

AF:

0.233

Gnomad4 NFE

AF:

0.192

Gnomad4 OTH

AF:

0.233

Alfa

AF:

0.205

Hom.:

2350

Bravo

AF:

0.257

Asia WGS

AF:

0.311

AC:

1084

AN:

3478

EpiCase

AF:

0.180

EpiControl

AF:

0.184

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency in ESP (all): 3199/12518=25.55% -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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