Genetic Variant ENST00000457002.1:n.137G>A (chr20-16586557-C-T) – ACMG Classification: Benign (-12 pts)

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

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)

RPLP0P1 links:

ENSG00000273998 (HGNC:):

ENSG00000273998 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=-0.55).

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	Effect	Exon rank	TSL
RPLP0P1	ENST00000457002.1 link	n.137G>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000273998	ENST00000773496.1 link	n.840C>T	non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000273998	ENST00000773497.1 link	n.*233C>T	downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.526

AC:

79785

AN:

151560

Hom.:

21541

Cov.:

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.:

Cov.:

AF XY:

0.494

AC XY:

178

AN XY:

360

show subpopulations

African (AFR)

AF:

0.417

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.667

AC:

AN:

East Asian (EAS)

AF:

0.389

AC:

AN:

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AF:

0.617

AC:

132

AN:

214

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.465

AC:

133

AN:

286

Other (OTH)

AF:

0.447

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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.:

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

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

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

(source)

DANN

Benign

0.51

PhyloP100

0.031

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over