19-15890405-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001082.5(CYP4F2):c.554G>T(p.Gly185Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0484 in 1,613,994 control chromosomes in the GnomAD database, including 2,286 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 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.554G>T | p.Gly185Val | missense_variant | 6/13 | ENST00000221700.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP4F2 | ENST00000221700.11 | c.554G>T | p.Gly185Val | missense_variant | 6/13 | 1 | NM_001082.5 | P3 | |
CYP4F2 | ENST00000011989.11 | c.554G>T | p.Gly185Val | missense_variant | 6/13 | 1 | A1 | ||
CYP4F2 | ENST00000392846.7 | n.497G>T | non_coding_transcript_exon_variant | 4/11 | 2 | ||||
CYP4F2 | ENST00000587671.2 | c.*139G>T | 3_prime_UTR_variant, NMD_transcript_variant | 5/8 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0490 AC: 7452AN: 152142Hom.: 197 Cov.: 32
GnomAD3 exomes AF: 0.0461 AC: 11595AN: 251462Hom.: 380 AF XY: 0.0458 AC XY: 6218AN XY: 135902
GnomAD4 exome AF: 0.0483 AC: 70591AN: 1461734Hom.: 2087 Cov.: 31 AF XY: 0.0477 AC XY: 34684AN XY: 727178
GnomAD4 genome AF: 0.0490 AC: 7467AN: 152260Hom.: 199 Cov.: 32 AF XY: 0.0488 AC XY: 3630AN XY: 74458
ClinVar
Submissions by phenotype
CYP4F2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 06, 2019 | This variant is classified as 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