Genetic Variant RRP1:c.*529A>G (chr21-43804303-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_003683.6(RRP1):c.*529A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 152,500 control chromosomes in the GnomAD database, including 27,963 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 0.58 ( 27914 hom., cov: 33)

Exomes 𝑓: 0.48 ( 49 hom. )

Consequence

RRP1
NM_003683.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.07

Publications

5 publications found

Variant links:

Genes affected

RRP1 (HGNC:18785): (ribosomal RNA processing 1) The protein encoded by this gene is the putative homolog of the yeast ribosomal RNA processing protein RRP1. The encoded protein is involved in the late stages of nucleologenesis at the end of mitosis, and may be required for the generation of 28S rRNA. [provided by RefSeq, Jul 2008]

RRP1 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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003683.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RRP1	NM_003683.6	MANE Select	c.*529A>G		3_prime_UTR	Exon 13 of 13	NP_003674.1	P56182

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
RRP1	ENST00000497547.2	TSL:1 MANE Select	c.*529A>G	3_prime_UTR	Exon 13 of 13	ENSP00000417464.1	P56182
RRP1	ENST00000467112.5	TSL:1	n.2029A>G	non_coding_transcript_exon	Exon 10 of 10
RRP1	ENST00000471909.1	TSL:1	n.1554A>G	non_coding_transcript_exon	Exon 8 of 8

Frequencies

GnomAD3 genomes

AF:

0.581

AC:

88253

AN:

152010

Hom.:

27861

Cov.:

show subpopulations

Gnomad AFR

AF:

0.805

Gnomad AMI

AF:

0.617

Gnomad AMR

AF:

0.643

Gnomad ASJ

AF:

0.478

Gnomad EAS

AF:

0.759

Gnomad SAS

AF:

0.729

Gnomad FIN

AF:

0.465

Gnomad MID

AF:

0.564

Gnomad NFE

AF:

0.429

Gnomad OTH

AF:

0.563

GnomAD4 exome

AF:

0.478

AC:

177

AN:

370

Hom.:

Cov.:

AF XY:

0.472

AC XY:

102

AN XY:

216

show subpopulations

African (AFR)

AF:

0.875

AC:

AN:

American (AMR)

AF:

0.667

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.667

AC:

AN:

East Asian (EAS)

AF:

0.800

AC:

AN:

South Asian (SAS)

AF:

0.750

AC:

AN:

European-Finnish (FIN)

AF:

0.385

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.449

AC:

AN:

214

Other (OTH)

AF:

0.417

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

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:

0.581

AC:

88362

AN:

152130

Hom.:

27914

Cov.:

AF XY:

0.586

AC XY:

43577

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.804

AC:

33401

AN:

41520

American (AMR)

AF:

0.644

AC:

9840

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.478

AC:

1658

AN:

3470

East Asian (EAS)

AF:

0.760

AC:

3930

AN:

5174

South Asian (SAS)

AF:

0.727

AC:

3507

AN:

4822

European-Finnish (FIN)

AF:

0.465

AC:

4907

AN:

10562

Middle Eastern (MID)

AF:

0.561

AC:

165

AN:

294

European-Non Finnish (NFE)

AF:

0.429

AC:

29187

AN:

67970

Other (OTH)

AF:

0.569

AC:

1204

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1737

3474

5210

6947

8684

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

726

1452

2178

2904

3630

<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:

0.536

Hom.:

4230

Bravo

AF:

0.604

Asia WGS

AF:

0.751

AC:

2612

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.1

(source)

DANN

Benign

0.38

PhyloP100

-2.1

Mutation Taster

=98/2

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over