chr6-46639654-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016593.5(CYP39A1):āc.328A>Gā(p.Asn110Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000168 in 1,611,308 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_016593.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP39A1 | NM_016593.5 | c.328A>G | p.Asn110Asp | missense_variant | 3/12 | ENST00000275016.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP39A1 | ENST00000275016.3 | c.328A>G | p.Asn110Asp | missense_variant | 3/12 | 1 | NM_016593.5 | P1 | |
CYP39A1 | ENST00000619708.4 | c.-28-1676A>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000485 AC: 12AN: 247630Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 133962
GnomAD4 exome AF: 0.00000891 AC: 13AN: 1459140Hom.: 0 Cov.: 30 AF XY: 0.00000827 AC XY: 6AN XY: 725880
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 13, 2022 | The c.328A>G (p.N110D) alteration is located in exon 3 (coding exon 3) of the CYP39A1 gene. This alteration results from a A to G substitution at nucleotide position 328, causing the asparagine (N) at amino acid position 110 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