chr15-82282319-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001348699.2(SAXO2):c.634C>T(p.Arg212Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000533 in 1,614,152 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_001348699.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SAXO2 | NM_001348699.2 | c.634C>T | p.Arg212Cys | missense_variant | Exon 4 of 4 | ENST00000682753.1 | NP_001335628.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SAXO2 | ENST00000682753.1 | c.634C>T | p.Arg212Cys | missense_variant | Exon 4 of 4 | NM_001348699.2 | ENSP00000508095.1 | |||
SAXO2 | ENST00000339465.5 | c.454C>T | p.Arg152Cys | missense_variant | Exon 3 of 3 | 1 | ENSP00000340445.5 | |||
SAXO2 | ENST00000565501.1 | n.745C>T | non_coding_transcript_exon_variant | Exon 3 of 3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000795 AC: 20AN: 251450Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135896
GnomAD4 exome AF: 0.0000547 AC: 80AN: 1461884Hom.: 0 Cov.: 31 AF XY: 0.0000688 AC XY: 50AN XY: 727244
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74444
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.454C>T (p.R152C) alteration is located in exon 3 (coding exon 3) of the SAXO2 gene. This alteration results from a C to T substitution at nucleotide position 454, causing the arginine (R) at amino acid position 152 to be replaced by a cysteine (C). 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