chr2-158094571-A-G

Position:

• chr2-158094571-A-G

Variant summary

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

The NM_001135098.2(UPP2):​c.148-7469A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 152,064 control chromosomes in the GnomAD database, including 38,749 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 0.71 (38749 hom., cov: 32)
• Consequence: UPP2 NM_001135098.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

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=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UPP2	NM_001135098.2	c.148-7469A>G		intron_variant			NP_001128570.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UPP2	ENST00000605860.5	c.148-7469A>G		intron_variant		5		ENSP00000474090.1

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107919 AN: 151946 Hom.: 38728 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.710 AC: 107986 AN: 152064 Hom.: 38749 Cov.: 32 AF XY: 0.702 AC XY: 52199 AN XY: 74310

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.728

Alfa AF: 0.714 Hom.: 7841

Bravo AF: 0.714

Asia WGS AF: 0.530 AC: 1847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	13
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6437129; hg19: chr2-158951083;