rs10183640

Variant names:

• chr2-157923692-G-A
• rs10183640
• ENST00000605860.5:c.-20+46964G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UPP2	ENST00000605860.5	c.-20+46964G>A		intron_variant	Intron 1 of 9	5		ENSP00000474090.1
UPP2	ENST00000489438.2	n.-20+46976G>A		intron_variant	Intron 1 of 9	3		ENSP00000520425.1

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

African (AFR) AF: 0.299 AC: 12361 AN: 41410

American (AMR) AF: 0.214 AC: 3274 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 915 AN: 3472

East Asian (EAS) AF: 0.372 AC: 1922 AN: 5170

South Asian (SAS) AF: 0.267 AC: 1286 AN: 4820

European-Finnish (FIN) AF: 0.327 AC: 3437 AN: 10522

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23307 AN: 67956

Other (OTH) AF: 0.298 AC: 630 AN: 2114

Alfa AF: 0.326 Hom.: 13380

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
PhyloP100		-0.0090
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10183640; hg19: chr2-158780204;