chr2-218782021-C-T
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000494263.5(CYP27A1):n.273C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000428 in 934,290 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000494263.5 non_coding_transcript_exon
Scores
Clinical Significance
Conservation
Publications
- cerebrotendinous xanthomatosisInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Myriad Women’s Health, Genomics England PanelApp, G2P
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYP27A1 | ENST00000494263.5 | n.273C>T | non_coding_transcript_exon_variant | Exon 1 of 7 | 2 | |||||
CYP27A1 | ENST00000258415.9 | c.-162C>T | upstream_gene_variant | 1 | NM_000784.4 | ENSP00000258415.4 | ||||
CYP27A1 | ENST00000445971.1 | n.-162C>T | upstream_gene_variant | 5 | ENSP00000404945.1 | |||||
CYP27A1 | ENST00000466602.1 | n.-153C>T | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152226Hom.: 0 Cov.: 32 show subpopulations
GnomAD4 exome AF: 0.00000384 AC: 3AN: 782064Hom.: 0 Cov.: 10 AF XY: 0.00000256 AC XY: 1AN XY: 390172 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74360 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Cholestanol storage disease Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at