chr19-15879401-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001082.5(CYP4F2):c.1342G>A(p.Glu448Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000102 in 1,460,218 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001082.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP4F2 | NM_001082.5 | c.1342G>A | p.Glu448Lys | missense_variant | 12/13 | ENST00000221700.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP4F2 | ENST00000221700.11 | c.1342G>A | p.Glu448Lys | missense_variant | 12/13 | 1 | NM_001082.5 | P3 | |
CYP4F2 | ENST00000011989.11 | c.1342G>A | p.Glu448Lys | missense_variant | 12/13 | 1 | A1 | ||
CYP4F2 | ENST00000589654.2 | c.132G>A | p.Gln44= | synonymous_variant | 2/3 | 3 | |||
CYP4F2 | ENST00000392846.7 | n.1285G>A | non_coding_transcript_exon_variant | 10/11 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 17AN: 151958Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251350Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135836
GnomAD4 exome AF: 0.000102 AC: 149AN: 1460218Hom.: 0 Cov.: 33 AF XY: 0.000102 AC XY: 74AN XY: 726352
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000112 AC: 17AN: 152076Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 25, 2024 | The c.1342G>A (p.E448K) alteration is located in exon 12 (coding exon 11) of the CYP4F2 gene. This alteration results from a G to A substitution at nucleotide position 1342, causing the glutamic acid (E) at amino acid position 448 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at