Variant rs2275580 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015179.4(RRP12):c.3433G>A(p.Gly1145Ser) variant causes a missense change. The variant allele was found at a frequency of 0.562 in 1,610,472 control chromosomes in the GnomAD database, including 261,545 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.46 ( 18591 hom., cov: 29)

Exomes 𝑓: 0.57 ( 242954 hom. )

Consequence

RRP12
NM_015179.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.49

Variant links:

Genes affected

RRP12 (HGNC:29100): (ribosomal RNA processing 12 homolog) Enables RNA binding activity. Predicted to be involved in rRNA processing. Located in cytosol; nucleolus; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

RRP12 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.9788742E-4).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
RRP12	NM_015179.4 linkuse as main transcript	c.3433G>A	p.Gly1145Ser	missense_variant	29/34	ENST00000370992.9
RRP12	NM_001145114.1 linkuse as main transcript	c.3250G>A	p.Gly1084Ser	missense_variant	27/32
RRP12	NM_001284337.2 linkuse as main transcript	c.3133G>A	p.Gly1045Ser	missense_variant	26/31
RRP12	XM_047424903.1 linkuse as main transcript	c.3349G>A	p.Gly1117Ser	missense_variant	28/33

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RRP12	ENST00000370992.9 linkuse as main transcript	c.3433G>A	p.Gly1145Ser	missense_variant	29/34	1	NM_015179.4	P1	Q5JTH9-1

Frequencies

GnomAD3 genomes

AF:

0.465

AC:

70406

AN:

151346

Hom.:

18595

Cov.:

show subpopulations

Gnomad AFR

AF:

0.201

Gnomad AMI

AF:

0.552

Gnomad AMR

AF:

0.537

Gnomad ASJ

AF:

0.543

Gnomad EAS

AF:

0.419

Gnomad SAS

AF:

0.470

Gnomad FIN

AF:

0.544

Gnomad MID

AF:

0.491

Gnomad NFE

AF:

0.595

Gnomad OTH

AF:

0.499

GnomAD3 exomes

AF:

0.538

AC:

134388

AN:

249570

Hom.:

37798

AF XY:

0.542

AC XY:

73169

AN XY:

135060

show subpopulations

Gnomad AFR exome

AF:

0.197

Gnomad AMR exome

AF:

0.597

Gnomad ASJ exome

AF:

0.554

Gnomad EAS exome

AF:

0.427

Gnomad SAS exome

AF:

0.486

Gnomad FIN exome

AF:

0.554

Gnomad NFE exome

AF:

0.597

Gnomad OTH exome

AF:

0.551

GnomAD4 exome

AF:

0.572

AC:

834076

AN:

1459008

Hom.:

242954

Cov.:

AF XY:

0.570

AC XY:

413884

AN XY:

725928

show subpopulations

Gnomad4 AFR exome

AF:

0.186

Gnomad4 AMR exome

AF:

0.590

Gnomad4 ASJ exome

AF:

0.551

Gnomad4 EAS exome

AF:

0.412

Gnomad4 SAS exome

AF:

0.487

Gnomad4 FIN exome

AF:

0.556

Gnomad4 NFE exome

AF:

0.598

Gnomad4 OTH exome

AF:

0.537

GnomAD4 genome

AF:

0.465

AC:

70407

AN:

151464

Hom.:

18591

Cov.:

AF XY:

0.464

AC XY:

34302

AN XY:

73928

show subpopulations

Gnomad4 AFR

AF:

0.200

Gnomad4 AMR

AF:

0.537

Gnomad4 ASJ

AF:

0.543

Gnomad4 EAS

AF:

0.419

Gnomad4 SAS

AF:

0.472

Gnomad4 FIN

AF:

0.544

Gnomad4 NFE

AF:

0.594

Gnomad4 OTH

AF:

0.498

Alfa

AF:

0.567

Hom.:

58962

Bravo

AF:

0.453

TwinsUK

AF:

0.584

AC:

2167

ALSPAC

AF:

0.604

AC:

2329

ESP6500AA

AF:

0.211

AC:

928

ESP6500EA

AF:

0.597

AC:

5136

ExAC

AF:

0.534

AC:

64827

Asia WGS

AF:

0.424

AC:

1473

AN:

3478

EpiCase

AF:

0.593

EpiControl

AF:

0.595

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.097

BayesDel_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.43

Cadd

Benign

Dann

Uncertain

1.0

DEOGEN2

Benign

0.18

T;.;T;.;T

Eigen

Uncertain

0.29

Eigen_PC

Uncertain

0.36

FATHMM_MKL

Uncertain

0.95

MetaRNN

Benign

0.00020

T;T;T;T;T

MetaSVM

Benign

-0.93

MutationAssessor

Uncertain

2.0

M;.;M;.;.

MutationTaster

Benign

0.0000071

P;P;P;P

PrimateAI

Benign

0.41

REVEL

Benign

0.12

Sift4G

Benign

0.28

T;T;T;T;T

Polyphen

0.94

P;B;P;.;.

Vest4

0.15

MPC

0.29

ClinPred

0.029

GERP RS

4.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.23

gMVP

0.11

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over