2-72132402-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_019885.4(CYP26B1):c.1364C>T(p.Ala455Val) variant causes a missense change. The variant allele was found at a frequency of 0.000036 in 1,611,742 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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 -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYP26B1 | ENST00000001146.7 | c.1364C>T | p.Ala455Val | missense_variant | Exon 6 of 6 | 1 | NM_019885.4 | ENSP00000001146.2 | ||
CYP26B1 | ENST00000546307.5 | c.1139C>T | p.Ala380Val | missense_variant | Exon 5 of 5 | 1 | ENSP00000443304.1 | |||
CYP26B1 | ENST00000412253.1 | c.791C>T | p.Ala264Val | missense_variant | Exon 5 of 5 | 1 | ENSP00000401465.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248774Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134830
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1459552Hom.: 0 Cov.: 32 AF XY: 0.0000331 AC XY: 24AN XY: 725708
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1364C>T (p.A455V) alteration is located in exon 6 (coding exon 6) of the CYP26B1 gene. This alteration results from a C to T substitution at nucleotide position 1364, causing the alanine (A) at amino acid position 455 to be replaced by a valine (V). 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