rs2241057
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_019885.4(CYP26B1):āc.791T>Cā(p.Leu264Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 1,614,020 control chromosomes in the GnomAD database, including 23,829 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_019885.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP26B1 | NM_019885.4 | c.791T>C | p.Leu264Ser | missense_variant | 4/6 | ENST00000001146.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP26B1 | ENST00000001146.7 | c.791T>C | p.Leu264Ser | missense_variant | 4/6 | 1 | NM_019885.4 | P1 | |
CYP26B1 | ENST00000546307.5 | c.566T>C | p.Leu189Ser | missense_variant | 3/5 | 1 | |||
CYP26B1 | ENST00000412253.1 | c.218T>C | p.Leu73Ser | missense_variant | 3/5 | 1 | |||
CYP26B1 | ENST00000474509.1 | downstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.192 AC: 29139AN: 152054Hom.: 3187 Cov.: 33
GnomAD3 exomes AF: 0.169 AC: 42396AN: 251358Hom.: 4391 AF XY: 0.159 AC XY: 21667AN XY: 135852
GnomAD4 exome AF: 0.162 AC: 236273AN: 1461848Hom.: 20613 Cov.: 35 AF XY: 0.158 AC XY: 114852AN XY: 727226
GnomAD4 genome ? AF: 0.192 AC: 29213AN: 152172Hom.: 3216 Cov.: 33 AF XY: 0.189 AC XY: 14029AN XY: 74396
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 08, 2018 | This variant is associated with the following publications: (PMID: 22415012) - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at