6-46636438-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.683A>Gā(p.Lys228Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,610,388 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.683A>G | p.Lys228Arg | missense_variant | 5/12 | ENST00000275016.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP39A1 | ENST00000275016.3 | c.683A>G | p.Lys228Arg | missense_variant | 5/12 | 1 | NM_016593.5 | P1 | |
CYP39A1 | ENST00000619708.4 | c.167A>G | p.Lys56Arg | missense_variant | 4/11 | 1 | |||
CYP39A1 | ENST00000480804.1 | n.102A>G | non_coding_transcript_exon_variant | 2/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 248992Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134528
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1458166Hom.: 0 Cov.: 29 AF XY: 0.0000166 AC XY: 12AN XY: 725060
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74390
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at