rs532333777
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PVS1_SupportingPM2
The NM_001278739.2(CYP39A1):c.1A>G(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,612,268 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_001278739.2 start_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYP39A1 | ENST00000619708.4 | c.1A>G | p.Met1? | start_lost | Exon 3 of 11 | 1 | ENSP00000477769.1 | |||
CYP39A1 | ENST00000275016.3 | c.517A>G | p.Met173Val | missense_variant | Exon 4 of 12 | 1 | NM_016593.5 | ENSP00000275016.2 | ||
CYP39A1 | ENST00000480804.1 | n.-65A>G | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249330Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134696
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460118Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726318
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.517A>G (p.M173V) alteration is located in exon 4 (coding exon 4) of the CYP39A1 gene. This alteration results from a A to G substitution at nucleotide position 517, causing the methionine (M) at amino acid position 173 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