Variant 21-43797678-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_003683.6(RRP1):c.600T>C(p.Ile200=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 1,613,566 control chromosomes in the GnomAD database, including 201,027 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 ( 27610 hom., cov: 32)

Exomes 𝑓: 0.47 ( 173417 hom. )

Consequence

RRP1
NM_003683.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.28

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP7

Synonymous conserved (PhyloP=-2.28 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RRP1	NM_003683.6 linkuse as main transcript	c.600T>C	p.Ile200=	synonymous_variant	7/13	ENST00000497547.2
RRP1	XM_017028485.3 linkuse as main transcript	c.600T>C	p.Ile200=	synonymous_variant	7/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
RRP1	ENST00000497547.2 linkuse as main transcript	c.600T>C	p.Ile200=	synonymous_variant	7/13	1	NM_003683.6	P1
RRP1	ENST00000467112.5 linkuse as main transcript	n.714T>C		non_coding_transcript_exon_variant	4/10	1
RRP1	ENST00000471909.1 linkuse as main transcript	n.239T>C		non_coding_transcript_exon_variant	2/8	1
RRP1	ENST00000483896.5 linkuse as main transcript	c.*503T>C		3_prime_UTR_variant, NMD_transcript_variant	8/9	3

Frequencies

GnomAD3 genomes

AF:

0.577

AC:

87637

AN:

151900

Hom.:

27556

Cov.:

show subpopulations

Gnomad AFR

AF:

0.803

Gnomad AMI

AF:

0.577

Gnomad AMR

AF:

0.638

Gnomad ASJ

AF:

0.477

Gnomad EAS

AF:

0.759

Gnomad SAS

AF:

0.728

Gnomad FIN

AF:

0.463

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.424

Gnomad OTH

AF:

0.559

GnomAD3 exomes

AF:

0.564

AC:

140497

AN:

249106

Hom.:

42713

AF XY:

0.556

AC XY:

75112

AN XY:

135204

show subpopulations

Gnomad AFR exome

AF:

0.811

Gnomad AMR exome

AF:

0.740

Gnomad ASJ exome

AF:

0.477

Gnomad EAS exome

AF:

0.751

Gnomad SAS exome

AF:

0.723

Gnomad FIN exome

AF:

0.465

Gnomad NFE exome

AF:

0.432

Gnomad OTH exome

AF:

0.522

GnomAD4 exome

AF:

0.473

AC:

690960

AN:

1461548

Hom.:

173417

Cov.:

AF XY:

0.478

AC XY:

347606

AN XY:

727108

show subpopulations

Gnomad4 AFR exome

AF:

0.808

Gnomad4 AMR exome

AF:

0.727

Gnomad4 ASJ exome

AF:

0.483

Gnomad4 EAS exome

AF:

0.764

Gnomad4 SAS exome

AF:

0.718

Gnomad4 FIN exome

AF:

0.464

Gnomad4 NFE exome

AF:

0.421

Gnomad4 OTH exome

AF:

0.505

GnomAD4 genome

AF:

0.577

AC:

87746

AN:

152018

Hom.:

27610

Cov.:

AF XY:

0.583

AC XY:

43317

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.803

Gnomad4 AMR

AF:

0.638

Gnomad4 ASJ

AF:

0.477

Gnomad4 EAS

AF:

0.759

Gnomad4 SAS

AF:

0.727

Gnomad4 FIN

AF:

0.463

Gnomad4 NFE

AF:

0.424

Gnomad4 OTH

AF:

0.565

Alfa

AF:

0.469

Hom.:

21065

Bravo

AF:

0.600

Asia WGS

AF:

0.751

AC:

2610

AN:

3478

EpiCase

AF:

0.429

EpiControl

AF:

0.436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.11

DANN

Benign

0.54

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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