chr19-15525446-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_173483.4(CYP4F22):c.110G>T(p.Arg37Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,613,982 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173483.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP4F22 | NM_173483.4 | c.110G>T | p.Arg37Leu | missense_variant | 3/14 | ENST00000269703.8 | |
CYP4F22 | XM_011527692.3 | c.110G>T | p.Arg37Leu | missense_variant | 4/15 | ||
CYP4F22 | XM_011527693.3 | c.110G>T | p.Arg37Leu | missense_variant | 3/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP4F22 | ENST00000269703.8 | c.110G>T | p.Arg37Leu | missense_variant | 3/14 | 2 | NM_173483.4 | P1 | |
CYP4F22 | ENST00000601005.2 | c.110G>T | p.Arg37Leu | missense_variant | 1/12 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251402Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135872
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461820Hom.: 0 Cov.: 32 AF XY: 0.0000248 AC XY: 18AN XY: 727210
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74334
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 24, 2022 | This sequence change replaces arginine, which is basic and polar, with leucine, which is neutral and non-polar, at codon 37 of the CYP4F22 protein (p.Arg37Leu). This variant is present in population databases (rs746979996, gnomAD 0.008%). This variant has not been reported in the literature in individuals affected with CYP4F22-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at