12-120199160-C-T

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

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 4.99
Variant links:
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]

Genome browser will be placed here

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
RPLP0NM_001002.4 linkc.276G>A p.Lys92Lys synonymous_variant Exon 4 of 8 ENST00000392514.9 NP_000993.1 P05388-1A0A024RBS2
RPLP0NM_053275.4 linkc.276G>A p.Lys92Lys synonymous_variant Exon 4 of 8 NP_444505.1 P05388-1A0A024RBS2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RPLP0ENST00000392514.9 linkc.276G>A p.Lys92Lys synonymous_variant Exon 4 of 8 1 NM_001002.4 ENSP00000376299.4 P05388-1

Frequencies

GnomAD3 genomes
AF:
0.00578
AC:
880
AN:
152192
Hom.:
4
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00183
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00255
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00331
Gnomad FIN
AF:
0.00358
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0102
Gnomad OTH
AF:
0.00621
GnomAD2 exomes
AF:
0.00645
AC:
1621
AN:
251480
AF XY:
0.00658
show subpopulations
Gnomad AFR exome
AF:
0.00129
Gnomad AMR exome
AF:
0.00278
Gnomad ASJ exome
AF:
0.000298
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00416
Gnomad NFE exome
AF:
0.0114
Gnomad OTH exome
AF:
0.00635
GnomAD4 exome
AF:
0.00960
AC:
14030
AN:
1461754
Hom.:
96
Cov.:
32
AF XY:
0.00929
AC XY:
6755
AN XY:
727186
show subpopulations
Gnomad4 AFR exome
AF:
0.00119
AC:
40
AN:
33480
Gnomad4 AMR exome
AF:
0.00277
AC:
124
AN:
44724
Gnomad4 ASJ exome
AF:
0.000153
AC:
4
AN:
26136
Gnomad4 EAS exome
AF:
0.00
AC:
0
AN:
39700
Gnomad4 SAS exome
AF:
0.00235
AC:
203
AN:
86258
Gnomad4 FIN exome
AF:
0.00425
AC:
227
AN:
53420
Gnomad4 NFE exome
AF:
0.0117
AC:
12967
AN:
1111878
Gnomad4 Remaining exome
AF:
0.00730
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
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.00578
AC:
880
AN:
152310
Hom.:
4
Cov.:
32
AF XY:
0.00498
AC XY:
371
AN XY:
74484
show subpopulations
Gnomad4 AFR
AF:
0.00183
AC:
0.00182824
AN:
0.00182824
Gnomad4 AMR
AF:
0.00255
AC:
0.00254935
AN:
0.00254935
Gnomad4 ASJ
AF:
0.00
AC:
0
AN:
0
Gnomad4 EAS
AF:
0.00
AC:
0
AN:
0
Gnomad4 SAS
AF:
0.00332
AC:
0.00331538
AN:
0.00331538
Gnomad4 FIN
AF:
0.00358
AC:
0.00357815
AN:
0.00357815
Gnomad4 NFE
AF:
0.0102
AC:
0.0102482
AN:
0.0102482
Gnomad4 OTH
AF:
0.00615
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
Variant carriers
0
20
40
60
80
100
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.00874
Hom.:
3
Bravo
AF:
0.00569
Asia WGS
AF:
0.00144
AC:
5
AN:
3478
EpiCase
AF:
0.00911
EpiControl
AF:
0.0102

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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.28
CADD
Benign
12
DANN
Benign
0.90
Mutation Taster
=48/52
disease causing

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs148524502; hg19: chr12-120636963; COSMIC: COSV56106507; COSMIC: COSV56106507; API