rs3902857

Variant names:

• chr1-218337512-T-C
• rs3902857
• NM_016052.4:c.*6421T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RRP15	NM_016052.4	c.*6421T>C		3_prime_UTR_variant	Exon 5 of 5	ENST00000366932.4	NP_057136.2
RRP15	XM_047421798.1	c.*6421T>C		3_prime_UTR_variant	Exon 5 of 5		XP_047277754.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RRP15	ENST00000366932.4	c.*6421T>C		3_prime_UTR_variant	Exon 5 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0534 AC: 2218 AN: 41548

American (AMR) AF: 0.0256 AC: 391 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0288 AC: 100 AN: 3470

East Asian (EAS) AF: 0.0797 AC: 413 AN: 5180

South Asian (SAS) AF: 0.0108 AC: 52 AN: 4818

European-Finnish (FIN) AF: 0.0221 AC: 235 AN: 10620

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0361 AC: 2456 AN: 68014

Other (OTH) AF: 0.0378 AC: 80 AN: 2114

Alfa AF: 0.0382 Hom.: 216

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
PhyloP100		-0.22
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: rs3902857; hg19: chr1-218510854;