chr20-4182555-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_175839.3(SMOX):c.1076G>A(p.Arg359His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000093 in 1,613,630 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R359S) has been classified as Uncertain significance.
Frequency
Consequence
NM_175839.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMOX | NM_175839.3 | c.1076G>A | p.Arg359His | missense_variant | 5/7 | ENST00000305958.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMOX | ENST00000305958.9 | c.1076G>A | p.Arg359His | missense_variant | 5/7 | 1 | NM_175839.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151946Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251192Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135748
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461684Hom.: 0 Cov.: 50 AF XY: 0.00000688 AC XY: 5AN XY: 727122
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151946Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74198
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | The c.1076G>A (p.R359H) alteration is located in exon 5 (coding exon 4) of the SMOX gene. This alteration results from a G to A substitution at nucleotide position 1076, causing the arginine (R) at amino acid position 359 to be replaced by a histidine (H). 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