19-15878779-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001082.5(CYP4F2):c.1555C>A(p.Leu519Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0626 in 1,611,242 control chromosomes in the GnomAD database, including 1,872 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001082.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP4F2 | NM_001082.5 | c.1555C>A | p.Leu519Met | missense_variant | 13/13 | ENST00000221700.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP4F2 | ENST00000221700.11 | c.1555C>A | p.Leu519Met | missense_variant | 13/13 | 1 | NM_001082.5 | P3 | |
CYP4F2 | ENST00000011989.11 | c.1555C>A | p.Leu519Met | missense_variant | 13/13 | 1 | A1 | ||
CYP4F2 | ENST00000589654.2 | c.*120C>A | 3_prime_UTR_variant | 3/3 | 3 | ||||
CYP4F2 | ENST00000392846.7 | n.1498C>A | non_coding_transcript_exon_variant | 11/11 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0777 AC: 11771AN: 151540Hom.: 409 Cov.: 32
GnomAD3 exomes AF: 0.0526 AC: 12982AN: 246596Hom.: 287 AF XY: 0.0509 AC XY: 6814AN XY: 133800
GnomAD4 exome AF: 0.0610 AC: 89089AN: 1459586Hom.: 1461 Cov.: 33 AF XY: 0.0601 AC XY: 43650AN XY: 726136
GnomAD4 genome AF: 0.0777 AC: 11781AN: 151656Hom.: 411 Cov.: 32 AF XY: 0.0766 AC XY: 5683AN XY: 74158
ClinVar
Submissions by phenotype
CYP4F2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 05, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at