12-11267869-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001394862.1(PRB3):c.380G>A(p.Gly127Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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 (★).
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 7)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PRB3
NM_001394862.1 missense
NM_001394862.1 missense
Scores
1
14
Clinical Significance
Conservation
PhyloP100: -1.35
Genes affected
PRB3 (HGNC:9339): (proline rich protein BstNI subfamily 3) This gene encodes a member of the heterogeneous family of basic, proline-rich, human salivary glycoproteins. Multiple alleles of this gene exhibiting variations in the length of the tandem repeats have been identified. The reference genome encodes the "Long" allele. The protein isoforms encoded by this gene are recognized as the "first line of oral defense" against the detrimental effects of polyphenols in the diet and pathogen infections. This gene is located in a cluster of closely related salivary proline-rich proteins on chromosome 12. [provided by RefSeq, Nov 2015]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.07941747).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRB3 | NM_001394862.1 | c.380G>A | p.Gly127Glu | missense_variant | 3/4 | ENST00000538488.3 | |
LOC107987435 | XR_007063209.1 | n.761-9601C>T | intron_variant, non_coding_transcript_variant | ||||
PRB3 | NM_006249.5 | c.380G>A | p.Gly127Glu | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRB3 | ENST00000538488.3 | c.380G>A | p.Gly127Glu | missense_variant | 3/4 | 5 | NM_001394862.1 | P1 | |
PRB3 | ENST00000539835.1 | n.387G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 48836Hom.: 0 Cov.: 7 FAILED QC
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GnomAD3 exomes AF: 0.00000894 AC: 2AN: 223770Hom.: 0 AF XY: 0.00000823 AC XY: 1AN XY: 121538
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000272 AC: 2AN: 735430Hom.: 0 Cov.: 9 AF XY: 0.00 AC XY: 0AN XY: 390026
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GnomAD4 genome ? Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 48860Hom.: 0 Cov.: 7 AF XY: 0.00 AC XY: 0AN XY: 23876
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 13, 2023 | The c.380G>A (p.G127E) 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 380, causing the glycine (G) at amino acid position 127 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:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D
REVEL
Benign
Sift4G
Benign
T;D
Vest4
MutPred
Gain of catalytic residue at P124 (P = 5e-04);Gain of catalytic residue at P124 (P = 5e-04);
MVP
MPC
ClinPred
T
GERP RS
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at