chr12-113053979-C-T

Variant names:

• chr12-113053979-C-T
• rs7956193
• ENST00000460336.1:n.-83C>T

Variant summary

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

The ENST00000460336.1(RPS15AP32):​n.-83C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 150,914 control chromosomes in the GnomAD database, including 6,539 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 0.29 (6538 hom., cov: 27)
  • Exomes 𝑓: 0.33 (1 hom.)
• Consequence: RPS15AP32 ENST00000460336.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650

Genes affected

RPS15AP32 (HGNC:35879): (ribosomal protein S15a pseudogene 32)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.315 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
RPS15AP32	ENST00000460336.1	n.-83C>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43055 AN: 150790 Hom.: 6541 Cov.: 27

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.0234

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.438

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.313

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 1 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 0.333

GnomAD4 genome AF: 0.285 AC: 43070 AN: 150908 Hom.: 6538 Cov.: 27 AF XY: 0.274 AC XY: 20187 AN XY: 73578

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.0235

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.314

Alfa AF: 0.301 Hom.: 856

Bravo AF: 0.293

Asia WGS AF: 0.128 AC: 446 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.3
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7956193; hg19: chr12-113491784;