12-11353279-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The ENST00000500254.6(PRB1):c.425G>A(p.Arg142Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000763 in 1,573,254 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000500254.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRB1 | NR_160307.2 | n.862G>A | non_coding_transcript_exon_variant | Exon 3 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRB1 | ENST00000500254.6 | c.425G>A | p.Arg142Gln | missense_variant | Exon 4 of 5 | 1 | ENSP00000420826.2 | |||
PRB1 | ENST00000545626.5 | c.365G>A | p.Arg122Gln | missense_variant | Exon 4 of 5 | 1 | ENSP00000444249.1 | |||
PRB1 | ENST00000240636.10 | n.*368G>A | non_coding_transcript_exon_variant | Exon 3 of 4 | 1 | ENSP00000485971.1 | ||||
PRB1 | ENST00000240636.10 | n.*368G>A | 3_prime_UTR_variant | Exon 3 of 4 | 1 | ENSP00000485971.1 |
Frequencies
GnomAD3 genomes AF: 0.0000147 AC: 2AN: 135908Hom.: 0 Cov.: 21
GnomAD3 exomes AF: 0.0000761 AC: 19AN: 249594Hom.: 1 AF XY: 0.0000740 AC XY: 10AN XY: 135056
GnomAD4 exome AF: 0.0000821 AC: 118AN: 1437346Hom.: 5 Cov.: 89 AF XY: 0.0000699 AC XY: 50AN XY: 715442
GnomAD4 genome AF: 0.0000147 AC: 2AN: 135908Hom.: 0 Cov.: 21 AF XY: 0.0000151 AC XY: 1AN XY: 66038
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.824G>A (p.R275Q) alteration is located in exon 3 (coding exon 3) of the PRB1 gene. This alteration results from a G to A substitution at nucleotide position 824, causing the arginine (R) at amino acid position 275 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