chr20-46545436-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_080721.3(OCSTAMP):c.938C>A(p.Thr313Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000387 in 1,550,834 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign 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. T313M) has been classified as Uncertain significance.
Frequency
Consequence
NM_080721.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OCSTAMP | NM_080721.3 | c.938C>A | p.Thr313Lys | missense_variant | 2/3 | ENST00000279028.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OCSTAMP | ENST00000279028.3 | c.938C>A | p.Thr313Lys | missense_variant | 2/3 | 5 | NM_080721.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000129 AC: 2AN: 155054Hom.: 0 AF XY: 0.0000121 AC XY: 1AN XY: 82332
GnomAD4 exome AF: 0.00000286 AC: 4AN: 1398648Hom.: 0 Cov.: 34 AF XY: 0.00000435 AC XY: 3AN XY: 689862
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2021 | The c.938C>A (p.T313K) alteration is located in exon 2 (coding exon 2) of the OCSTAMP gene. This alteration results from a C to A substitution at nucleotide position 938, causing the threonine (T) at amino acid position 313 to be replaced by a lysine (K). 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