chr20-46541373-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_080721.3(OCSTAMP):c.1602T>A(p.His534Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000195 in 856,804 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/20 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OCSTAMP | NM_080721.3 | c.1602T>A | p.His534Gln | missense_variant | 3/3 | ENST00000279028.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OCSTAMP | ENST00000279028.3 | c.1602T>A | p.His534Gln | missense_variant | 3/3 | 5 | NM_080721.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000283 AC: 43AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000266 AC: 41AN: 153966Hom.: 0 AF XY: 0.000184 AC XY: 15AN XY: 81730
GnomAD4 exome AF: 0.000176 AC: 124AN: 704488Hom.: 0 Cov.: 9 AF XY: 0.000159 AC XY: 59AN XY: 371498
GnomAD4 genome AF: 0.000282 AC: 43AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.000362 AC XY: 27AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | The c.1602T>A (p.H534Q) alteration is located in exon 3 (coding exon 3) of the OCSTAMP gene. This alteration results from a T to A substitution at nucleotide position 1602, causing the histidine (H) at amino acid position 534 to be replaced by a glutamine (Q). 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