rs369202988
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_StrongBP7
The NM_001394862.1(PRB3):c.792A>T(p.Pro264Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P264P) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.0000084 ( 0 hom., cov: 17)
Exomes 𝑓: 0.0000082 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PRB3
NM_001394862.1 synonymous
NM_001394862.1 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0380
Publications
3 publications found
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 was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP7
Synonymous conserved (PhyloP=0.038 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001394862.1. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PRB3 | NM_001394862.1 | MANE Select | c.792A>T | p.Pro264Pro | synonymous | Exon 3 of 4 | NP_001381791.1 | Q04118 | |
| PRB3 | NM_006249.5 | c.666A>T | p.Pro222Pro | synonymous | Exon 4 of 5 | NP_006240.4 | A0A0G2JNB4 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PRB3 | ENST00000538488.3 | TSL:5 MANE Select | c.792A>T | p.Pro264Pro | synonymous | Exon 3 of 4 | ENSP00000442626.2 | Q04118 |
Frequencies
GnomAD3 genomes 0.00000839 AC: 1AN: 119186Hom.: 0 Cov.: 17 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
119186
Hom.:
Cov.:
17
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000819 AC: 11AN: 1343012Hom.: 0 Cov.: 44 AF XY: 0.00 AC XY: 0AN XY: 664612 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
11
AN:
1343012
Hom.:
Cov.:
44
AF XY:
AC XY:
0
AN XY:
664612
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
30922
American (AMR)
AF:
AC:
0
AN:
41228
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
22620
East Asian (EAS)
AF:
AC:
2
AN:
30014
South Asian (SAS)
AF:
AC:
0
AN:
78430
European-Finnish (FIN)
AF:
AC:
1
AN:
44952
Middle Eastern (MID)
AF:
AC:
0
AN:
4934
European-Non Finnish (NFE)
AF:
AC:
8
AN:
1036190
Other (OTH)
AF:
AC:
0
AN:
53722
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.248
Heterozygous variant carriers
0
2
3
5
6
8
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
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4
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<30
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>80
Age
GnomAD4 genome 0.00000838 AC: 1AN: 119308Hom.: 0 Cov.: 17 AF XY: 0.0000175 AC XY: 1AN XY: 57300 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
1
AN:
119308
Hom.:
Cov.:
17
AF XY:
AC XY:
1
AN XY:
57300
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
31960
American (AMR)
AF:
AC:
0
AN:
12010
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2952
East Asian (EAS)
AF:
AC:
0
AN:
3070
South Asian (SAS)
AF:
AC:
0
AN:
2750
European-Finnish (FIN)
AF:
AC:
1
AN:
7300
Middle Eastern (MID)
AF:
AC:
0
AN:
218
European-Non Finnish (NFE)
AF:
AC:
0
AN:
56684
Other (OTH)
AF:
AC:
0
AN:
1586
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.325
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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