rs10183640

Positions:

• chr2-157923692-G-A

Variant summary

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

The ENST00000605860.5(UPP2):​c.-20+46964G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,942 control chromosomes in the GnomAD database, including 7,594 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 0.31 (7594 hom., cov: 32)
• Consequence: UPP2 ENST00000605860.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900

Genes affected

UPP2 (HGNC:23061): (uridine phosphorylase 2) Enables deoxyuridine phosphorylase activity; identical protein binding activity; and uridine phosphorylase activity. Involved in dCMP catabolic process and uridine catabolic process. Located in type III intermediate filament. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UPP2	ENST00000605860.5	c.-20+46964G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47500 AN: 151824 Hom.: 7586 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.313 AC: 47521 AN: 151942 Hom.: 7594 Cov.: 32 AF XY: 0.311 AC XY: 23078 AN XY: 74248

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.298

Alfa AF: 0.327 Hom.: 8294

Bravo AF: 0.302

Asia WGS AF: 0.331 AC: 1151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10183640; hg19: chr2-158780204;