chr4-186191867-T-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_207352.4(CYP4V2):c.44T>C(p.Leu15Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000455 in 1,586,806 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_207352.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP4V2 | NM_207352.4 | c.44T>C | p.Leu15Pro | missense_variant | 1/11 | ENST00000378802.5 | |
CYP4V2 | XM_005262935.5 | c.44T>C | p.Leu15Pro | missense_variant | 1/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP4V2 | ENST00000378802.5 | c.44T>C | p.Leu15Pro | missense_variant | 1/11 | 1 | NM_207352.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000309 AC: 47AN: 152108Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000296 AC: 59AN: 199626Hom.: 0 AF XY: 0.000309 AC XY: 34AN XY: 110050
GnomAD4 exome AF: 0.000471 AC: 675AN: 1434580Hom.: 0 Cov.: 30 AF XY: 0.000459 AC XY: 327AN XY: 712354
GnomAD4 genome ? AF: 0.000309 AC: 47AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.000215 AC XY: 16AN XY: 74438
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.44T>C (p.L15P) alteration is located in exon 1 (coding exon 1) of the CYP4V2 gene. This alteration results from a T to C substitution at nucleotide position 44, causing the leucine (L) at amino acid position 15 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 25, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at