2-158043030-C-T

Variant names:

• chr2-158043030-C-T
• rs2355164
• NM_001135098.2:c.147+27144C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001135098.2(UPP2):​c.147+27144C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,192 control chromosomes in the GnomAD database, including 4,599 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 0.21 (4599 hom., cov: 32)
• Consequence: UPP2 NM_001135098.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.84
• Publications: 6 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001135098.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UPP2	NM_001135098.2		c.147+27144C>T		intron	N/A	NP_001128570.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UPP2	ENST00000605860.5	TSL:5	c.147+27144C>T		intron	N/A	ENSP00000474090.1
	UPP2	ENST00000890004.1		c.-25+27144C>T		intron	N/A	ENSP00000560063.1
	UPP2	ENST00000489438.2	TSL:3	n.147+27144C>T		intron	N/A	ENSP00000520425.1

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32543 AN: 152074 Hom.: 4597 Cov.: 32

Gnomad AFR AF: 0.0526

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.214 AC: 32553 AN: 152192 Hom.: 4599 Cov.: 32 AF XY: 0.225 AC XY: 16732 AN XY: 74402

African (AFR) AF: 0.0527 AC: 2189 AN: 41550

American (AMR) AF: 0.294 AC: 4494 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 789 AN: 3470

East Asian (EAS) AF: 0.471 AC: 2426 AN: 5154

South Asian (SAS) AF: 0.392 AC: 1889 AN: 4822

European-Finnish (FIN) AF: 0.321 AC: 3397 AN: 10582

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16829 AN: 68000

Other (OTH) AF: 0.203 AC: 430 AN: 2114

Alfa AF: 0.248 Hom.: 3723

Bravo AF: 0.202

Asia WGS AF: 0.392 AC: 1361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	14
DANN	Benign	0.70
PhyloP100		1.8
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: rs2355164; hg19: chr2-158899542;