2-218782191-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_000784.4(CYP27A1):c.9G>A(p.Ala3Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000722 in 1,384,744 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 Likely benign (★★).
Frequency
Consequence
NM_000784.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYP27A1 | ENST00000258415.9 | c.9G>A | p.Ala3Ala | synonymous_variant | Exon 1 of 9 | 1 | NM_000784.4 | ENSP00000258415.4 | ||
CYP27A1 | ENST00000445971.1 | n.9G>A | non_coding_transcript_exon_variant | Exon 1 of 5 | 5 | ENSP00000404945.1 | ||||
CYP27A1 | ENST00000466602.1 | n.18G>A | non_coding_transcript_exon_variant | Exon 1 of 3 | 2 | |||||
CYP27A1 | ENST00000494263.5 | n.443G>A | non_coding_transcript_exon_variant | Exon 1 of 7 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000750 AC: 1AN: 133360Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 72774
GnomAD4 exome AF: 7.22e-7 AC: 1AN: 1384744Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 683408
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Cholestanol storage disease Benign:1
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Cardiovascular phenotype Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at