chr12-11268067-G-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001394862.1(PRB3):āc.182C>Gā(p.Pro61Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00127 in 150,980 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P61T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001394862.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRB3 | NM_001394862.1 | c.182C>G | p.Pro61Arg | missense_variant | 3/4 | ENST00000538488.3 | |
LOC107987435 | XR_007063209.1 | n.761-9403G>C | intron_variant, non_coding_transcript_variant | ||||
PRB3 | NM_006249.5 | c.182C>G | p.Pro61Arg | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRB3 | ENST00000538488.3 | c.182C>G | p.Pro61Arg | missense_variant | 3/4 | 5 | NM_001394862.1 | P1 | |
PRB3 | ENST00000539835.1 | n.189C>G | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00127 AC: 192AN: 150870Hom.: 0 Cov.: 28
GnomAD3 exomes AF: 0.000284 AC: 71AN: 249842Hom.: 0 AF XY: 0.000288 AC XY: 39AN XY: 135420
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000275 AC: 399AN: 1449996Hom.: 1 Cov.: 41 AF XY: 0.000274 AC XY: 198AN XY: 721350
GnomAD4 genome AF: 0.00127 AC: 192AN: 150980Hom.: 0 Cov.: 28 AF XY: 0.00144 AC XY: 106AN XY: 73758
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 09, 2021 | The c.182C>G (p.P61R) alteration is located in exon 3 (coding exon 3) of the PRB3 gene. This alteration results from a C to G substitution at nucleotide position 182, causing the proline (P) at amino acid position 61 to be replaced by an arginine (R). 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