ENST00000457002.1:n.137G>A

Variant summary

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

The ENST00000457002.1(RPLP0P1):​n.137G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 152,266 control chromosomes in the GnomAD database, including 21,657 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 0.53 ( 21570 hom., cov: 32)
Exomes 𝑓: 0.52 ( 87 hom. )

Consequence

RPLP0P1
ENST00000457002.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0310

Publications

3 publications found
Variant links:
Genes affected
RPLP0P1 (HGNC:16585): (ribosomal protein lateral stalk subunit P0 pseudogene 1)

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=-0.55).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RPLP0P1 n.16586557C>T intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RPLP0P1ENST00000457002.1 linkn.137G>A non_coding_transcript_exon_variant Exon 1 of 1 6
ENSG00000273998ENST00000773496.1 linkn.840C>T non_coding_transcript_exon_variant Exon 2 of 2
ENSG00000273998ENST00000773497.1 linkn.*233C>T downstream_gene_variant

Frequencies

GnomAD3 genomes
AF:
0.526
AC:
79785
AN:
151560
Hom.:
21541
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.627
Gnomad AMI
AF:
0.413
Gnomad AMR
AF:
0.467
Gnomad ASJ
AF:
0.408
Gnomad EAS
AF:
0.595
Gnomad SAS
AF:
0.485
Gnomad FIN
AF:
0.596
Gnomad MID
AF:
0.446
Gnomad NFE
AF:
0.475
Gnomad OTH
AF:
0.478
GnomAD4 exome
AF:
0.517
AC:
304
AN:
588
Hom.:
87
Cov.:
0
AF XY:
0.494
AC XY:
178
AN XY:
360
show subpopulations
African (AFR)
AF:
0.417
AC:
5
AN:
12
American (AMR)
AF:
1.00
AC:
4
AN:
4
Ashkenazi Jewish (ASJ)
AF:
0.667
AC:
4
AN:
6
East Asian (EAS)
AF:
0.389
AC:
7
AN:
18
South Asian (SAS)
AF:
0.250
AC:
2
AN:
8
European-Finnish (FIN)
AF:
0.617
AC:
132
AN:
214
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2
European-Non Finnish (NFE)
AF:
0.465
AC:
133
AN:
286
Other (OTH)
AF:
0.447
AC:
17
AN:
38
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
7
14
21
28
35
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
2
4
6
8
10
<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:
0.527
AC:
79868
AN:
151678
Hom.:
21570
Cov.:
32
AF XY:
0.528
AC XY:
39139
AN XY:
74134
show subpopulations
African (AFR)
AF:
0.627
AC:
25826
AN:
41162
American (AMR)
AF:
0.467
AC:
7122
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
0.408
AC:
1415
AN:
3470
East Asian (EAS)
AF:
0.594
AC:
3062
AN:
5156
South Asian (SAS)
AF:
0.485
AC:
2334
AN:
4814
European-Finnish (FIN)
AF:
0.596
AC:
6277
AN:
10540
Middle Eastern (MID)
AF:
0.435
AC:
128
AN:
294
European-Non Finnish (NFE)
AF:
0.475
AC:
32312
AN:
67958
Other (OTH)
AF:
0.481
AC:
1015
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1927
3854
5782
7709
9636
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
698
1396
2094
2792
3490
<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:
0.464
Hom.:
8596
Bravo
AF:
0.525
Asia WGS
AF:
0.549
AC:
1906
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.55
CADD
Benign
4.3
DANN
Benign
0.51
PhyloP100
0.031

Splicing

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

Publications

Other links and lift over

dbSNP: rs3746786; hg19: chr20-16567202; API