rs7585982

Positions:

• chr2-158119084-G-A

Variant summary

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

The NM_173355.4(UPP2):​c.454+1146G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,774 control chromosomes in the GnomAD database, including 24,137 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 0.56 (24137 hom., cov: 32)
• Consequence: UPP2 NM_173355.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UPP2	NM_173355.4	c.454+1146G>A		intron_variant		ENST00000005756.5
UPP2	NM_001135098.2	c.625+1146G>A		intron_variant
UPP2	XM_017003484.2	c.454+1146G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UPP2	ENST00000005756.5	c.454+1146G>A		intron_variant		1	NM_173355.4	P1
UPP2	ENST00000605860.5	c.625+1146G>A		intron_variant		5
UPP2	ENST00000460456.1	n.377-4665G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84230 AN: 151656 Hom.: 24115 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.555 AC: 84287 AN: 151774 Hom.: 24137 Cov.: 32 AF XY: 0.551 AC XY: 40880 AN XY: 74198

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.576

Alfa AF: 0.560 Hom.: 3247

Bravo AF: 0.556

Asia WGS AF: 0.378 AC: 1316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.64
DANN	Benign	0.20

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7585982; hg19: chr2-158975596;