20-46541528-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_080721.3(OCSTAMP):c.1447G>A(p.Asp483Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000759 in 1,551,738 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_080721.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OCSTAMP | NM_080721.3 | c.1447G>A | p.Asp483Asn | missense_variant | 3/3 | ENST00000279028.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OCSTAMP | ENST00000279028.3 | c.1447G>A | p.Asp483Asn | missense_variant | 3/3 | 5 | NM_080721.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000453 AC: 69AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000305 AC: 47AN: 154134Hom.: 0 AF XY: 0.000293 AC XY: 24AN XY: 81778
GnomAD4 exome AF: 0.000792 AC: 1109AN: 1399390Hom.: 2 Cov.: 31 AF XY: 0.000751 AC XY: 518AN XY: 690204
GnomAD4 genome AF: 0.000453 AC: 69AN: 152348Hom.: 0 Cov.: 33 AF XY: 0.000362 AC XY: 27AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | The c.1447G>A (p.D483N) alteration is located in exon 3 (coding exon 3) of the OCSTAMP gene. This alteration results from a G to A substitution at nucleotide position 1447, causing the aspartic acid (D) at amino acid position 483 to be replaced by an asparagine (N). 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