chr12-11267992-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001394862.1(PRB3):c.257G>A(p.Gly86Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000277 in 1,445,798 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/17 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. G86R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001394862.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRB3 | NM_001394862.1 | c.257G>A | p.Gly86Glu | missense_variant | 3/4 | ENST00000538488.3 | |
LOC107987435 | XR_007063209.1 | n.761-9478C>T | intron_variant, non_coding_transcript_variant | ||||
PRB3 | NM_006249.5 | c.257G>A | p.Gly86Glu | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRB3 | ENST00000538488.3 | c.257G>A | p.Gly86Glu | missense_variant | 3/4 | 5 | NM_001394862.1 | P1 | |
PRB3 | ENST00000539835.1 | n.264G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 21
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249676Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135456
GnomAD4 exome AF: 0.00000277 AC: 4AN: 1445798Hom.: 0 Cov.: 34 AF XY: 0.00000556 AC XY: 4AN XY: 718894
GnomAD4 genome ? Cov.: 21
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2022 | The c.257G>A (p.G86E) alteration is located in exon 3 (coding exon 3) of the PRB3 gene. This alteration results from a G to A substitution at nucleotide position 257, causing the glycine (G) at amino acid position 86 to be replaced by a glutamic acid (E). 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