16-29234781-C-T

Variant names:

• chr16-29234781-C-T
• rs194045
• ENST00000641956.1:n.422-16698C>T

Variant summary

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

The ENST00000641956.1(RRN3P2):​n.422-16698C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,110 control chromosomes in the GnomAD database, including 2,436 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 0.18 (2436 hom., cov: 32)
• Consequence: RRN3P2 ENST00000641956.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.195 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	ENST00000641956.1	n.422-16698C>T		intron_variant	Intron 1 of 7
RRN3P2	ENST00000691488.2	n.82-16698C>T		intron_variant	Intron 1 of 2
RRN3P2	ENST00000768495.1	n.517-16698C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27030 AN: 151992 Hom.: 2430 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.0818

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.178 AC: 27058 AN: 152110 Hom.: 2436 Cov.: 32 AF XY: 0.175 AC XY: 13011 AN XY: 74362

African (AFR) AF: 0.191 AC: 7928 AN: 41482

American (AMR) AF: 0.200 AC: 3065 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 619 AN: 3466

East Asian (EAS) AF: 0.0821 AC: 424 AN: 5162

South Asian (SAS) AF: 0.180 AC: 870 AN: 4828

European-Finnish (FIN) AF: 0.131 AC: 1391 AN: 10582

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12066 AN: 67978

Other (OTH) AF: 0.185 AC: 391 AN: 2114

Alfa AF: 0.175 Hom.: 6106

Bravo AF: 0.183

Asia WGS AF: 0.141 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.71
PhyloP100		-1.3

Splicing

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

Publications

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Other links and lift over

dbSNP: rs194045; hg19: chr16-29246102;