chr3-58534958-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_003500.4(ACOX2):c.149G>A(p.Arg50His) variant causes a missense change. The variant allele was found at a frequency of 0.0000198 in 1,614,066 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R50C) has been classified as Uncertain significance.
Frequency
Consequence
NM_003500.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACOX2 | NM_003500.4 | c.149G>A | p.Arg50His | missense_variant | 2/15 | ENST00000302819.10 | |
ACOX2 | XM_047449042.1 | c.347G>A | p.Arg116His | missense_variant | 2/15 | ||
ACOX2 | XM_005265505.2 | c.149G>A | p.Arg50His | missense_variant | 2/15 | ||
ACOX2 | XM_006713340.4 | c.-16G>A | 5_prime_UTR_variant | 1/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACOX2 | ENST00000302819.10 | c.149G>A | p.Arg50His | missense_variant | 2/15 | 1 | NM_003500.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 251160Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135788
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461846Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727224
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74352
ClinVar
Submissions by phenotype
Congenital bile acid synthesis defect 6 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Dec 20, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at