ENST00000562902.3:n.353-46612T>C

Variant names:

• chr16-29170869-T-C
• rs12933229
• ENST00000562902.3:n.353-46612T>C

Variant summary

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

The ENST00000562902.3(RRN3P2):​n.353-46612T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,210 control chromosomes in the GnomAD database, including 5,495 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 0.26 (5495 hom., cov: 33)
• Consequence: RRN3P2 ENST00000562902.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65
• Publications: 12 publications found

Genes affected

RRN3P2 (HGNC:37619): (RRN3 pseudogene 2) Predicted to enable RNA polymerase I core binding activity and RNA polymerase I general transcription initiation factor activity. Predicted to be involved in transcription initiation from RNA polymerase I promoter. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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 = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RRN3P2	ENST00000562902.3	n.353-46612T>C		intron_variant	Intron 2 of 2	2
RRN3P2	ENST00000563477.1	n.139+31070T>C		intron_variant	Intron 1 of 2	4
RRN3P2	ENST00000641956.1	n.421+31070T>C		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38895 AN: 152092 Hom.: 5494 Cov.: 33

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.296

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.256 AC: 38905 AN: 152210 Hom.: 5495 Cov.: 33 AF XY: 0.257 AC XY: 19095 AN XY: 74388

African (AFR) AF: 0.142 AC: 5900 AN: 41568

American (AMR) AF: 0.296 AC: 4529 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1059 AN: 3472

East Asian (EAS) AF: 0.362 AC: 1864 AN: 5156

South Asian (SAS) AF: 0.183 AC: 881 AN: 4826

European-Finnish (FIN) AF: 0.317 AC: 3354 AN: 10572

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20464 AN: 68004

Other (OTH) AF: 0.297 AC: 628 AN: 2116

Alfa AF: 0.291 Hom.: 11360

Bravo AF: 0.252

Asia WGS AF: 0.260 AC: 902 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	3.7
DANN	Benign	0.79
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs12933229; hg19: chr16-29182190;