rs880987

Variant names:

• chr21-43804574-C-T
• rs880987
• ENST00000467112.5:n.2300C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000467112.5(RRP1):​n.2300C>T 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 0.17 in 152,310 control chromosomes in the GnomAD database, including 2,960 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 0.17 (2956 hom., cov: 33)
  • Exomes 𝑓: 0.17 (4 hom.)
• Consequence: RRP1 ENST00000467112.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 6 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RRP1	NM_003683.6	c.*800C>T		3_prime_UTR_variant	Exon 13 of 13	ENST00000497547.2	NP_003674.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RRP1	ENST00000467112.5	n.2300C>T		non_coding_transcript_exon_variant	Exon 10 of 10	1
RRP1	ENST00000471909.1	n.1825C>T		non_coding_transcript_exon_variant	Exon 8 of 8	1
RRP1	ENST00000497547.2	c.*800C>T		3_prime_UTR_variant	Exon 13 of 13	1	NM_003683.6	ENSP00000417464.1

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25786 AN: 152086 Hom.: 2946 Cov.: 33

Gnomad AFR AF: 0.0491

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.174

GnomAD4 exome AF: 0.170 AC: 18 AN: 106 Hom.: 4 Cov.: 0 AF XY: 0.118 AC XY: 9 AN XY: 76

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.125 AC: 5 AN: 40

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.224 AC: 13 AN: 58

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.170 AC: 25809 AN: 152204 Hom.: 2956 Cov.: 33 AF XY: 0.177 AC XY: 13170 AN XY: 74382

African (AFR) AF: 0.0490 AC: 2038 AN: 41558

American (AMR) AF: 0.271 AC: 4136 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 596 AN: 3472

East Asian (EAS) AF: 0.470 AC: 2424 AN: 5162

South Asian (SAS) AF: 0.293 AC: 1411 AN: 4820

European-Finnish (FIN) AF: 0.257 AC: 2717 AN: 10580

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11714 AN: 68006

Other (OTH) AF: 0.179 AC: 379 AN: 2114

Alfa AF: 0.160 Hom.: 393

Bravo AF: 0.168

Asia WGS AF: 0.343 AC: 1193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.26
DANN	Benign	0.56
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs880987; hg19: chr21-45224455;