NM_019885.4:c.1509G>T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_019885.4(CYP26B1):c.1509G>T(p.Glu503Asp) variant causes a missense change. The variant allele was found at a frequency of 0.0000661 in 1,604,198 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_019885.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYP26B1 | ENST00000001146.7 | c.1509G>T | p.Glu503Asp | missense_variant | Exon 6 of 6 | 1 | NM_019885.4 | ENSP00000001146.2 | ||
CYP26B1 | ENST00000546307.5 | c.1284G>T | p.Glu428Asp | missense_variant | Exon 5 of 5 | 1 | ENSP00000443304.1 | |||
CYP26B1 | ENST00000412253.1 | c.936G>T | p.Glu312Asp | missense_variant | Exon 5 of 5 | 1 | ENSP00000401465.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000348 AC: 8AN: 229918Hom.: 0 AF XY: 0.0000242 AC XY: 3AN XY: 124194
GnomAD4 exome AF: 0.0000702 AC: 102AN: 1451974Hom.: 0 Cov.: 32 AF XY: 0.0000541 AC XY: 39AN XY: 721220
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152224Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74354
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1509G>T (p.E503D) alteration is located in exon 6 (coding exon 6) of the CYP26B1 gene. This alteration results from a G to T substitution at nucleotide position 1509, causing the glutamic acid (E) at amino acid position 503 to be replaced by an aspartic acid (D). 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