ENST00000460336.1:n.-83C>T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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

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) AF: 0.333 AC: 2 AN: 6

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.280 AC: 11531 AN: 41114

American (AMR) AF: 0.278 AC: 4195 AN: 15090

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1599 AN: 3460

East Asian (EAS) AF: 0.0235 AC: 121 AN: 5150

South Asian (SAS) AF: 0.138 AC: 658 AN: 4754

European-Finnish (FIN) AF: 0.217 AC: 2249 AN: 10362

Middle Eastern (MID) AF: 0.433 AC: 123 AN: 284

European-Non Finnish (NFE) AF: 0.318 AC: 21544 AN: 67710

Other (OTH) AF: 0.314 AC: 653 AN: 2080

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
PhyloP100		-0.065

Splicing

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

Other links and lift over

dbSNP: rs7956193; hg19: chr12-113491784;