Genetic Variant RPLP0P2:n.332+1729G>C (chr11-61632017-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000475331.1(RPLP0P2):n.332+1729G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 151,908 control chromosomes in the GnomAD database, including 10,673 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 0.36 ( 10673 hom., cov: 31)

Consequence

RPLP0P2
ENST00000475331.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.262

Publications

3 publications found

Variant links:

Genes affected

RPLP0P2 (HGNC:):

RPLP0P2 links:

RPLP0P2 (HGNC:17960): (ribosomal protein lateral stalk subunit P0 pseudogene 2)

RPLP0P2 links:

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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPLP0P2	NR_002775.2 link	n.434+2978G>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
RPLP0P2	ENST00000475331.1 link	n.332+1729G>C	intron_variant	Intron 2 of 2	4
RPLP0P2	ENST00000475561.5 link	n.387+1729G>C	intron_variant	Intron 2 of 2	4
RPLP0P2	ENST00000478959.1 link	n.433+2978G>C	intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes

AF:

0.361

AC:

54786

AN:

151790

Hom.:

10636

Cov.:

show subpopulations

Gnomad AFR

AF:

0.487

Gnomad AMI

AF:

0.360

Gnomad AMR

AF:

0.274

Gnomad ASJ

AF:

0.449

Gnomad EAS

AF:

0.0648

Gnomad SAS

AF:

0.230

Gnomad FIN

AF:

0.267

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.346

Gnomad OTH

AF:

0.355

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.361

AC:

54858

AN:

151908

Hom.:

10673

Cov.:

AF XY:

0.353

AC XY:

26201

AN XY:

74250

show subpopulations

African (AFR)

AF:

0.488

AC:

20201

AN:

41432

American (AMR)

AF:

0.273

AC:

4169

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.449

AC:

1554

AN:

3464

East Asian (EAS)

AF:

0.0647

AC:

335

AN:

5174

South Asian (SAS)

AF:

0.229

AC:

1106

AN:

4822

European-Finnish (FIN)

AF:

0.267

AC:

2817

AN:

10536

Middle Eastern (MID)

AF:

0.364

AC:

107

AN:

294

European-Non Finnish (NFE)

AF:

0.346

AC:

23505

AN:

67930

Other (OTH)

AF:

0.351

AC:

737

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1711

3423

5134

6846

8557

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

512

1024

1536

2048

2560

<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:

0.189

Hom.:

353

Bravo

AF:

0.369

Asia WGS

AF:

0.171

AC:

599

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.9

(source)

DANN

Benign

0.42

PhyloP100

-0.26

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over