rs11666601
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_173483.4(CYP4F22):c.582G>A(p.Ala194=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 1,613,962 control chromosomes in the GnomAD database, including 10,055 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.093 ( 744 hom., cov: 31)
Exomes 𝑓: 0.11 ( 9311 hom. )
Consequence
CYP4F22
NM_173483.4 synonymous
NM_173483.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.167
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
Variant 19-15537904-G-A is Benign according to our data. Variant chr19-15537904-G-A is described in ClinVar as [Benign]. Clinvar id is 262835.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-15537904-G-A is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=0.167 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP4F22 | NM_173483.4 | c.582G>A | p.Ala194= | synonymous_variant | 7/14 | ENST00000269703.8 | |
CYP4F22 | XM_011527692.3 | c.582G>A | p.Ala194= | synonymous_variant | 8/15 | ||
CYP4F22 | XM_011527693.3 | c.582G>A | p.Ala194= | synonymous_variant | 7/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP4F22 | ENST00000269703.8 | c.582G>A | p.Ala194= | synonymous_variant | 7/14 | 2 | NM_173483.4 | P1 | |
CYP4F22 | ENST00000601005.2 | c.582G>A | p.Ala194= | synonymous_variant | 5/12 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0930 AC: 14137AN: 152054Hom.: 742 Cov.: 31
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GnomAD3 exomes AF: 0.0960 AC: 24148AN: 251458Hom.: 1246 AF XY: 0.0991 AC XY: 13469AN XY: 135894
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GnomAD4 exome AF: 0.111 AC: 161862AN: 1461790Hom.: 9311 Cov.: 35 AF XY: 0.110 AC XY: 80312AN XY: 727190
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GnomAD4 genome AF: 0.0930 AC: 14156AN: 152172Hom.: 744 Cov.: 31 AF XY: 0.0921 AC XY: 6851AN XY: 74380
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Autosomal recessive congenital ichthyosis 5 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at