19-15525404-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_173483.4(CYP4F22):c.68C>T(p.Ala23Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000103 in 1,614,196 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A23T) has been classified as Uncertain significance.
Frequency
Consequence
NM_173483.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CYP4F22 | NM_173483.4 | c.68C>T | p.Ala23Val | missense_variant | Exon 3 of 14 | ENST00000269703.8 | NP_775754.2 | |
CYP4F22 | XM_011527692.3 | c.68C>T | p.Ala23Val | missense_variant | Exon 4 of 15 | XP_011525994.1 | ||
CYP4F22 | XM_011527693.3 | c.68C>T | p.Ala23Val | missense_variant | Exon 3 of 14 | XP_011525995.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000342 AC: 52AN: 152236Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000135 AC: 34AN: 251400Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135878
GnomAD4 exome AF: 0.0000780 AC: 114AN: 1461842Hom.: 0 Cov.: 32 AF XY: 0.0000784 AC XY: 57AN XY: 727234
GnomAD4 genome AF: 0.000341 AC: 52AN: 152354Hom.: 0 Cov.: 32 AF XY: 0.000349 AC XY: 26AN XY: 74492
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.68C>T (p.A23V) alteration is located in exon 3 (coding exon 1) of the CYP4F22 gene. This alteration results from a C to T substitution at nucleotide position 68, causing the alanine (A) at amino acid position 23 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at