Variant 19-15525307-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_173483.4(CYP4F22):c.-1-29A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0149 in 1,606,594 control chromosomes in the GnomAD database, including 388 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.030 ( 153 hom., cov: 32)

Exomes 𝑓: 0.013 ( 235 hom. )

Consequence

CYP4F22
NM_173483.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.116

Variant links:

Genes affected

CYP4F22 (HGNC:26820): (cytochrome P450 family 4 subfamily F member 22) 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 gene is part of a cluster of cytochrome P450 genes on chromosome 19 and encodes an enzyme thought to play a role in the 12(R)-lipoxygenase pathway. Mutations in this gene are the cause of ichthyosis lamellar type 3. [provided by RefSeq, Jul 2008]

CYP4F22 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 19-15525307-A-G is Benign according to our data. Variant chr19-15525307-A-G is described in ClinVar as [Benign]. Clinvar id is 1237700.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
CYP4F22	NM_173483.4 linkuse as main transcript	c.-1-29A>G	intron_variant	ENST00000269703.8
CYP4F22	XM_011527692.3 linkuse as main transcript	c.-1-29A>G	intron_variant
CYP4F22	XM_011527693.3 linkuse as main transcript	c.-1-29A>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP4F22	ENST00000269703.8 linkuse as main transcript	c.-1-29A>G		intron_variant		2	NM_173483.4	P1
CYP4F22	ENST00000601005.2 linkuse as main transcript			upstream_gene_variant		5		P1

Frequencies

GnomAD3 genomes

AF:

0.0295

AC:

4486

AN:

152108

Hom.:

154

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0783

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0138

Gnomad ASJ

AF:

0.0115

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00787

Gnomad FIN

AF:

0.000660

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0132

Gnomad OTH

AF:

0.0211

GnomAD3 exomes

AF:

0.0132

AC:

3233

AN:

244912

Hom.:

AF XY:

0.0121

AC XY:

1609

AN XY:

132746

show subpopulations

Gnomad AFR exome

AF:

0.0754

Gnomad AMR exome

AF:

0.00758

Gnomad ASJ exome

AF:

0.0109

Gnomad EAS exome

AF:

0.000165

Gnomad SAS exome

AF:

0.00729

Gnomad FIN exome

AF:

0.000897

Gnomad NFE exome

AF:

0.0121

Gnomad OTH exome

AF:

0.0114

GnomAD4 exome

AF:

0.0133

AC:

19394

AN:

1454368

Hom.:

235

Cov.:

AF XY:

0.0130

AC XY:

9426

AN XY:

723716

show subpopulations

Gnomad4 AFR exome

AF:

0.0800

Gnomad4 AMR exome

AF:

0.00900

Gnomad4 ASJ exome

AF:

0.0104

Gnomad4 EAS exome

AF:

0.000126

Gnomad4 SAS exome

AF:

0.00713

Gnomad4 FIN exome

AF:

0.000938

Gnomad4 NFE exome

AF:

0.0130

Gnomad4 OTH exome

AF:

0.0154

GnomAD4 genome

AF:

0.0295

AC:

4493

AN:

152226

Hom.:

153

Cov.:

AF XY:

0.0282

AC XY:

2098

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.0783

Gnomad4 AMR

AF:

0.0137

Gnomad4 ASJ

AF:

0.0115

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00767

Gnomad4 FIN

AF:

0.000660

Gnomad4 NFE

AF:

0.0132

Gnomad4 OTH

AF:

0.0209

Alfa

AF:

0.0181

Hom.:

Bravo

AF:

0.0320

Asia WGS

AF:

0.0110

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

7.3

DANN

Benign

0.67

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.16

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