2-158020401-C-T

Variant names:

• chr2-158020401-C-T
• rs17420138
• NM_001135098.2:c.147+4515C>T

Variant summary

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

The NM_001135098.2(UPP2):​c.147+4515C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0449 in 152,286 control chromosomes in the GnomAD database, including 204 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 0.045 (204 hom., cov: 32)
• Consequence: UPP2 NM_001135098.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.812

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 (NFE) allele frequency at 95% confidence interval = 0.0667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UPP2	NM_001135098.2	c.147+4515C>T		intron_variant	Intron 2 of 8		NP_001128570.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UPP2	ENST00000605860.5	c.147+4515C>T		intron_variant	Intron 3 of 9	5		ENSP00000474090.1

Frequencies

GnomAD3 genomes AF: 0.0450 AC: 6845 AN: 152168 Hom.: 205 Cov.: 32

Gnomad AFR AF: 0.0126

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0430

Gnomad ASJ AF: 0.0329

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0277

Gnomad FIN AF: 0.0608

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0683

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0449 AC: 6843 AN: 152286 Hom.: 204 Cov.: 32 AF XY: 0.0437 AC XY: 3252 AN XY: 74470

Gnomad4 AFR AF: 0.0126

Gnomad4 AMR AF: 0.0429

Gnomad4 ASJ AF: 0.0329

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0278

Gnomad4 FIN AF: 0.0608

Gnomad4 NFE AF: 0.0683

Gnomad4 OTH AF: 0.0440

Alfa AF: 0.0520 Hom.: 112

Bravo AF: 0.0412

Asia WGS AF: 0.0180 AC: 63 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	0.67
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17420138; hg19: chr2-158876913;