rs10483362

Variant names:

• chr14-30791724-C-T
• rs10483362
• ENST00000554665.1:n.209-9728G>A

Variant summary

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

The ENST00000554665.1(ENSG00000258558):​n.209-9728G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0136 in 152,122 control chromosomes in the GnomAD database, including 32 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 0.014 (32 hom., cov: 31)
• Consequence: ENSG00000258558 ENST00000554665.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.550
• Publications: 1 publications found

Genes affected

ENSG00000258558 (HGNC:):

RPL12P5 (HGNC:19669): (ribosomal protein L12 pseudogene 5)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0666 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554665.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258558	ENST00000554665.1	TSL:3	n.209-9728G>A		intron	N/A
	RPL12P5	ENST00000475149.1	TSL:6	n.*235C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0136 AC: 2062 AN: 152002 Hom.: 32 Cov.: 31

Gnomad AFR AF: 0.0133

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00989

Gnomad ASJ AF: 0.00952

Gnomad EAS AF: 0.0721

Gnomad SAS AF: 0.0547

Gnomad FIN AF: 0.000189

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.00925

Gnomad OTH AF: 0.0235

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

GnomAD4 genome AF: 0.0136 AC: 2065 AN: 152122 Hom.: 32 Cov.: 31 AF XY: 0.0145 AC XY: 1075 AN XY: 74370

African (AFR) AF: 0.0133 AC: 553 AN: 41492

American (AMR) AF: 0.00988 AC: 151 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00952 AC: 33 AN: 3466

East Asian (EAS) AF: 0.0726 AC: 375 AN: 5164

South Asian (SAS) AF: 0.0547 AC: 263 AN: 4808

European-Finnish (FIN) AF: 0.000189 AC: 2 AN: 10590

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00925 AC: 629 AN: 68000

Other (OTH) AF: 0.0228 AC: 48 AN: 2108

Alfa AF: 0.0118 Hom.: 19

Bravo AF: 0.0136

Asia WGS AF: 0.0730 AC: 254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.47
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs10483362; hg19: chr14-31260930;