2-157953923-G-T

Variant names:

• chr2-157953923-G-T
• rs12694942
• ENST00000605860.5:c.-19-41257G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000605860.5(UPP2):​c.-19-41257G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,590 control chromosomes in the GnomAD database, including 18,811 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 0.48 (18811 hom., cov: 29)
• Consequence: UPP2 ENST00000605860.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173
• Publications: 3 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 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.-19-41257G>T		intron_variant	Intron 1 of 9	5		ENSP00000474090.1
UPP2	ENST00000489438.2	n.-19-41257G>T		intron_variant	Intron 1 of 9	3		ENSP00000520425.1

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72742 AN: 151472 Hom.: 18787 Cov.: 29

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.362

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.480 AC: 72817 AN: 151590 Hom.: 18811 Cov.: 29 AF XY: 0.473 AC XY: 35025 AN XY: 74050

African (AFR) AF: 0.673 AC: 27832 AN: 41342

American (AMR) AF: 0.319 AC: 4857 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1459 AN: 3466

East Asian (EAS) AF: 0.468 AC: 2405 AN: 5138

South Asian (SAS) AF: 0.284 AC: 1361 AN: 4796

European-Finnish (FIN) AF: 0.430 AC: 4502 AN: 10462

Middle Eastern (MID) AF: 0.366 AC: 106 AN: 290

European-Non Finnish (NFE) AF: 0.427 AC: 28975 AN: 67866

Other (OTH) AF: 0.441 AC: 930 AN: 2108

Alfa AF: 0.396 Hom.: 2650

Bravo AF: 0.481

Asia WGS AF: 0.407 AC: 1414 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	0.92
DANN	Benign	0.24
PhyloP100		-0.17
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: rs12694942; hg19: chr2-158810435;