1-228211826-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001386125.1(OBSCN):c.43C>T(p.Arg15Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000446 in 1,568,666 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. R15G) has been classified as Uncertain significance.
Frequency
Consequence
NM_001386125.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OBSCN | NM_001386125.1 | c.43C>T | p.Arg15Trp | missense_variant | 2/116 | ENST00000680850.1 | NP_001373054.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OBSCN | ENST00000680850.1 | c.43C>T | p.Arg15Trp | missense_variant | 2/116 | NM_001386125.1 | ENSP00000505517.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152118Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000475 AC: 1AN: 210556Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 115578
GnomAD4 exome AF: 0.00000353 AC: 5AN: 1416548Hom.: 0 Cov.: 72 AF XY: 0.00000429 AC XY: 3AN XY: 698942
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152118Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 12, 2022 | The p.R15W variant (also known as c.43C>T), located in coding exon 1 of the OBSCN gene, results from a C to T substitution at nucleotide position 43. The arginine at codon 15 is replaced by tryptophan, an amino acid with dissimilar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at