rs10483362

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000258558 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000258558	ENST00000554665.1	n.209-9728G>A		intron_variant	Intron 1 of 2	3
RPL12P5	ENST00000475149.1	n.*235C>T		downstream_gene_variant		6

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

Gnomad4 AFR AF: 0.0133

Gnomad4 AMR AF: 0.00988

Gnomad4 ASJ AF: 0.00952

Gnomad4 EAS AF: 0.0726

Gnomad4 SAS AF: 0.0547

Gnomad4 FIN AF: 0.000189

Gnomad4 NFE AF: 0.00925

Gnomad4 OTH AF: 0.0228

Alfa AF: 0.0122 Hom.: 17

Bravo AF: 0.0136

Asia WGS AF: 0.0730 AC: 254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483362; hg19: chr14-31260930;