chr16-786030-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_058192.3(RPUSD1):c.859A>G(p.Thr287Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000233 in 1,499,932 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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. T287I) has been classified as Uncertain significance.
Frequency
Consequence
NM_058192.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPUSD1 | NM_058192.3 | c.859A>G | p.Thr287Ala | missense_variant | 6/6 | ENST00000007264.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPUSD1 | ENST00000007264.7 | c.859A>G | p.Thr287Ala | missense_variant | 6/6 | 2 | NM_058192.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151838Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000293 AC: 4AN: 136496Hom.: 0 AF XY: 0.0000134 AC XY: 1AN XY: 74674
GnomAD4 exome AF: 0.0000237 AC: 32AN: 1347976Hom.: 0 Cov.: 31 AF XY: 0.0000197 AC XY: 13AN XY: 660032
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 151956Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74272
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 27, 2023 | The c.859A>G (p.T287A) alteration is located in exon 6 (coding exon 5) of the RPUSD1 gene. This alteration results from a A to G substitution at nucleotide position 859, causing the threonine (T) at amino acid position 287 to be replaced by an alanine (A). 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