chr14-35387932-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000459899.1(RPLP0P3):​n.*189C>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,990 control chromosomes in the GnomAD database, including 11,824 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.39 ( 11824 hom., cov: 33)

Consequence

RPLP0P3
ENST00000459899.1 downstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.159

Publications

4 publications found
Variant links:
Genes affected
RPLP0P3 (HGNC:23558): (ribosomal protein lateral stalk subunit P0 pseudogene 3)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RPLP0P3ENST00000459899.1 linkn.*189C>A downstream_gene_variant 6

Frequencies

GnomAD3 genomes
AF:
0.388
AC:
58924
AN:
151872
Hom.:
11799
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.464
Gnomad AMI
AF:
0.371
Gnomad AMR
AF:
0.426
Gnomad ASJ
AF:
0.291
Gnomad EAS
AF:
0.273
Gnomad SAS
AF:
0.311
Gnomad FIN
AF:
0.481
Gnomad MID
AF:
0.256
Gnomad NFE
AF:
0.340
Gnomad OTH
AF:
0.344
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.388
AC:
59012
AN:
151990
Hom.:
11824
Cov.:
33
AF XY:
0.394
AC XY:
29251
AN XY:
74268
show subpopulations
African (AFR)
AF:
0.464
AC:
19230
AN:
41438
American (AMR)
AF:
0.427
AC:
6511
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
0.291
AC:
1007
AN:
3466
East Asian (EAS)
AF:
0.273
AC:
1409
AN:
5164
South Asian (SAS)
AF:
0.311
AC:
1501
AN:
4826
European-Finnish (FIN)
AF:
0.481
AC:
5077
AN:
10554
Middle Eastern (MID)
AF:
0.262
AC:
77
AN:
294
European-Non Finnish (NFE)
AF:
0.340
AC:
23124
AN:
67968
Other (OTH)
AF:
0.350
AC:
738
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1848
3695
5543
7390
9238
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
552
1104
1656
2208
2760
<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:
0.353
Hom.:
13651
Bravo
AF:
0.388

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.9
DANN
Benign
0.22
PhyloP100
0.16

Splicing

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

Publications

Other links and lift over

dbSNP: rs12891443; hg19: chr14-35857138; API