19-41121476-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000774.5(CYP2F1):c.503C>A(p.Thr168Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,459,904 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 Uncertain significance (★).
Frequency
Consequence
NM_000774.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYP2F1 | ENST00000331105.7 | c.503C>A | p.Thr168Lys | missense_variant | Exon 5 of 10 | 1 | NM_000774.5 | ENSP00000333534.2 | ||
CYP2F1 | ENST00000532164.2 | n.503C>A | non_coding_transcript_exon_variant | Exon 5 of 10 | 1 | ENSP00000471416.1 | ||||
CYP2F1 | ENST00000531409.5 | n.578C>A | non_coding_transcript_exon_variant | Exon 5 of 8 | 2 | |||||
CYP2F1 | ENST00000526093.5 | n.225-481C>A | intron_variant | Intron 2 of 3 | 4 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250472Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135414
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1459904Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726338
GnomAD4 genome Cov.: 30
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.503C>A (p.T168K) alteration is located in exon 5 (coding exon 4) of the CYP2F1 gene. This alteration results from a C to A substitution at nucleotide position 503, causing the threonine (T) at amino acid position 168 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