Genetic Variant RPL29P25:n.552G>A (chr12-110841836-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 ENST00000465069.2(RPL29P25):n.552G>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 0.0501 in 957,436 control chromosomes in the GnomAD database, including 1,705 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 0.071 ( 548 hom., cov: 32)

Exomes 𝑓: 0.046 ( 1157 hom. )

Consequence

RPL29P25
ENST00000465069.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.473

Publications

0 publications found

Variant links:

Genes affected

RPL29P25 (HGNC:37039): (ribosomal protein L29 pseudogene 25)

RPL29P25 links:

ENSG00000257268 (HGNC:):

ENSG00000257268 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL29P25		n.110841836C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL29P25	ENST00000465069.2 link	n.552G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000257268	ENST00000551161.1 link	n.217-3763C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.0714

AC:

10858

AN:

152046

Hom.:

547

Cov.:

show subpopulations

Gnomad AFR

AF:

0.145

Gnomad AMI

AF:

0.0592

Gnomad AMR

AF:

0.0458

Gnomad ASJ

AF:

0.0231

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0368

Gnomad FIN

AF:

0.0727

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0431

Gnomad OTH

AF:

0.0664

GnomAD4 exome

AF:

0.0461

AC:

37115

AN:

805272

Hom.:

1157

Cov.:

AF XY:

0.0457

AC XY:

18966

AN XY:

415244

show subpopulations

African (AFR)

AF:

0.153

AC:

2861

AN:

18748

American (AMR)

AF:

0.0390

AC:

1036

AN:

26534

Ashkenazi Jewish (ASJ)

AF:

0.0320

AC:

514

AN:

16060

East Asian (EAS)

AF:

0.000311

AC:

AN:

32140

South Asian (SAS)

AF:

0.0412

AC:

1870

AN:

45388

European-Finnish (FIN)

AF:

0.0709

AC:

2226

AN:

31410

Middle Eastern (MID)

AF:

0.0714

AC:

188

AN:

2634

European-Non Finnish (NFE)

AF:

0.0445

AC:

26489

AN:

595302

Other (OTH)

AF:

0.0518

AC:

1921

AN:

37056

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

1610

3220

4829

6439

8049

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

832

1664

2496

3328

4160

<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:

0.0714

AC:

10866

AN:

152164

Hom.:

548

Cov.:

AF XY:

0.0692

AC XY:

5150

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.144

AC:

5994

AN:

41486

American (AMR)

AF:

0.0456

AC:

698

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0231

AC:

AN:

3466

East Asian (EAS)

AF:

0.00

AC:

AN:

5180

South Asian (SAS)

AF:

0.0371

AC:

179

AN:

4828

European-Finnish (FIN)

AF:

0.0727

AC:

769

AN:

10578

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0431

AC:

2929

AN:

68008

Other (OTH)

AF:

0.0658

AC:

139

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

499

998

1498

1997

2496

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

118

236

354

472

590

<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:

0.0582

Hom.:

Bravo

AF:

0.0732

Asia WGS

AF:

0.0260

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.0

(source)

DANN

Benign

0.67

PhyloP100

-0.47

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