19-41116351-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000774.5(CYP2F1):c.163C>T(p.Leu55Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,614,052 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYP2F1 | ENST00000331105.7 | c.163C>T | p.Leu55Phe | missense_variant | Exon 2 of 10 | 1 | NM_000774.5 | ENSP00000333534.2 | ||
CYP2F1 | ENST00000532164.2 | n.163C>T | non_coding_transcript_exon_variant | Exon 2 of 10 | 1 | ENSP00000471416.1 | ||||
CYP2F1 | ENST00000531409.5 | n.238C>T | non_coding_transcript_exon_variant | Exon 2 of 8 | 2 | |||||
CYP2F1 | ENST00000526093.5 | n.62-104C>T | intron_variant | Intron 1 of 3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152164Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000111 AC: 28AN: 251156Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135726
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461770Hom.: 0 Cov.: 34 AF XY: 0.0000303 AC XY: 22AN XY: 727194
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152282Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.163C>T (p.L55F) alteration is located in exon 2 (coding exon 1) of the CYP2F1 gene. This alteration results from a C to T substitution at nucleotide position 163, causing the leucine (L) at amino acid position 55 to be replaced by a phenylalanine (F). 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