12-120199160-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_001002.4(RPLP0):c.276G>A(p.Lys92Lys) variant causes a synonymous change. The variant allele was found at a frequency of 0.00924 in 1,614,064 control chromosomes in the GnomAD database, including 100 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0058 ( 4 hom., cov: 32)
Exomes 𝑓: 0.0096 ( 96 hom. )
Consequence
RPLP0
NM_001002.4 synonymous
NM_001002.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.99
Genes affected
RPLP0 (HGNC:10371): (ribosomal protein lateral stalk subunit P0) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein, which is the functional equivalent of the E. coli L10 ribosomal protein, belongs to the L10P family of ribosomal proteins. It is a neutral phosphoprotein with a C-terminal end that is nearly identical to the C-terminal ends of the acidic ribosomal phosphoproteins P1 and P2. The P0 protein can interact with P1 and P2 to form a pentameric complex consisting of P1 and P2 dimers, and a P0 monomer. The protein is located in the cytoplasm. Transcript variants derived from alternative splicing exist; they encode the same protein. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.28).
BP6
Variant 12-120199160-C-T is Benign according to our data. Variant chr12-120199160-C-T is described in ClinVar as [Benign]. Clinvar id is 770414.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High AC in GnomAd4 at 880 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPLP0 | NM_001002.4 | c.276G>A | p.Lys92Lys | synonymous_variant | Exon 4 of 8 | ENST00000392514.9 | NP_000993.1 | |
RPLP0 | NM_053275.4 | c.276G>A | p.Lys92Lys | synonymous_variant | Exon 4 of 8 | NP_444505.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00578 AC: 880AN: 152192Hom.: 4 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
880
AN:
152192
Hom.:
Cov.:
32
Gnomad AFR
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GnomAD2 exomes AF: 0.00645 AC: 1621AN: 251480 AF XY: 0.00658 show subpopulations
GnomAD2 exomes
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AC:
1621
AN:
251480
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GnomAD4 exome AF: 0.00960 AC: 14030AN: 1461754Hom.: 96 Cov.: 32 AF XY: 0.00929 AC XY: 6755AN XY: 727186 show subpopulations
GnomAD4 exome
AF:
AC:
14030
AN:
1461754
Hom.:
Cov.:
32
AF XY:
AC XY:
6755
AN XY:
727186
Gnomad4 AFR exome
AF:
AC:
40
AN:
33480
Gnomad4 AMR exome
AF:
AC:
124
AN:
44724
Gnomad4 ASJ exome
AF:
AC:
4
AN:
26136
Gnomad4 EAS exome
AF:
AC:
0
AN:
39700
Gnomad4 SAS exome
AF:
AC:
203
AN:
86258
Gnomad4 FIN exome
AF:
AC:
227
AN:
53420
Gnomad4 NFE exome
AF:
AC:
12967
AN:
1111878
Gnomad4 Remaining exome
AF:
AC:
441
AN:
60390
Heterozygous variant carriers
0
639
1279
1918
2558
3197
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
488
976
1464
1952
2440
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Age
GnomAD4 genome AF: 0.00578 AC: 880AN: 152310Hom.: 4 Cov.: 32 AF XY: 0.00498 AC XY: 371AN XY: 74484 show subpopulations
GnomAD4 genome
AF:
AC:
880
AN:
152310
Hom.:
Cov.:
32
AF XY:
AC XY:
371
AN XY:
74484
Gnomad4 AFR
AF:
AC:
0.00182824
AN:
0.00182824
Gnomad4 AMR
AF:
AC:
0.00254935
AN:
0.00254935
Gnomad4 ASJ
AF:
AC:
0
AN:
0
Gnomad4 EAS
AF:
AC:
0
AN:
0
Gnomad4 SAS
AF:
AC:
0.00331538
AN:
0.00331538
Gnomad4 FIN
AF:
AC:
0.00357815
AN:
0.00357815
Gnomad4 NFE
AF:
AC:
0.0102482
AN:
0.0102482
Gnomad4 OTH
AF:
AC:
0.00614948
AN:
0.00614948
Heterozygous variant carriers
0
49
97
146
194
243
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
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Age
Alfa
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Asia WGS
AF:
AC:
5
AN:
3478
EpiCase
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EpiControl
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Mar 29, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=48/52
disease causing
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