chr14-35387932-G-T

Variant names:

• chr14-35387932-G-T
• rs12891443
• ENST00000459899.1:n.*189C>A

Variant summary

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

The ENST00000459899.1(RPLP0P3):​n.*189C>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,990 control chromosomes in the GnomAD database, including 11,824 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 0.39 (11824 hom., cov: 33)
• Consequence: RPLP0P3 ENST00000459899.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.159
• Publications: 4 publications found

Genes affected

RPLP0P3 (HGNC:23558): (ribosomal protein lateral stalk subunit P0 pseudogene 3)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 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
RPLP0P3	ENST00000459899.1	n.*189C>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58924 AN: 151872 Hom.: 11799 Cov.: 33

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.388 AC: 59012 AN: 151990 Hom.: 11824 Cov.: 33 AF XY: 0.394 AC XY: 29251 AN XY: 74268

African (AFR) AF: 0.464 AC: 19230 AN: 41438

American (AMR) AF: 0.427 AC: 6511 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1007 AN: 3466

East Asian (EAS) AF: 0.273 AC: 1409 AN: 5164

South Asian (SAS) AF: 0.311 AC: 1501 AN: 4826

European-Finnish (FIN) AF: 0.481 AC: 5077 AN: 10554

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23124 AN: 67968

Other (OTH) AF: 0.350 AC: 738 AN: 2110

Alfa AF: 0.353 Hom.: 13651

Bravo AF: 0.388

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.22
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs12891443; hg19: chr14-35857138;