rs3902857

Positions:

• chr1-218337512-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016052.4(RRP15):​c.*6421T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0393 in 152,264 control chromosomes in the GnomAD database, including 152 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 0.039 (152 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: RRP15 NM_016052.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

Genes affected

RRP15 (HGNC:24255): (ribosomal RNA processing 15 homolog) This gene encodes a protein that co-purifies with human nucleoli. A similar protein in budding yeast is a component of pre-60S ribosomal particles, and is required for the early maturation steps of the 60S subunit. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RRP15	NM_016052.4	c.*6421T>C		3_prime_UTR_variant	5/5	ENST00000366932.4	NP_057136.2
RRP15	XM_047421798.1	c.*6421T>C		3_prime_UTR_variant	5/5		XP_047277754.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RRP15	ENST00000366932.4	c.*6421T>C		3_prime_UTR_variant	5/5	1	NM_016052.4	ENSP00000355899.3

Frequencies

GnomAD3 genomes AF: 0.0393 AC: 5979 AN: 152146 Hom.: 152 Cov.: 33

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0257

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.0797

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.0221

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0361

Gnomad OTH AF: 0.0382

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0393 AC: 5983 AN: 152264 Hom.: 152 Cov.: 33 AF XY: 0.0375 AC XY: 2794 AN XY: 74460

Gnomad4 AFR AF: 0.0534

Gnomad4 AMR AF: 0.0256

Gnomad4 ASJ AF: 0.0288

Gnomad4 EAS AF: 0.0797

Gnomad4 SAS AF: 0.0108

Gnomad4 FIN AF: 0.0221

Gnomad4 NFE AF: 0.0361

Gnomad4 OTH AF: 0.0378

Alfa AF: 0.0370 Hom.: 46

Bravo AF: 0.0418

Asia WGS AF: 0.0250 AC: 88 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.3
DANN	Benign	0.75

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

Other links and lift over

dbSNP: rs3902857; hg19: chr1-218510854;