rs7585982

Variant names:

• chr2-158119084-G-A
• rs7585982
• NM_173355.4:c.454+1146G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173355.4. 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_173355.4	MANE Select	c.454+1146G>A		intron	N/A	NP_775491.1
	UPP2	NM_001135098.2		c.625+1146G>A		intron	N/A	NP_001128570.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UPP2	ENST00000005756.5	TSL:1 MANE Select	c.454+1146G>A		intron	N/A	ENSP00000005756.5
	UPP2	ENST00000605860.5	TSL:5	c.625+1146G>A		intron	N/A	ENSP00000474090.1
	UPP2	ENST00000460456.1	TSL:5	n.377-4665G>A		intron	N/A

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

African (AFR) AF: 0.581 AC: 24069 AN: 41446

American (AMR) AF: 0.551 AC: 8411 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1880 AN: 3466

East Asian (EAS) AF: 0.199 AC: 1030 AN: 5174

South Asian (SAS) AF: 0.460 AC: 2215 AN: 4812

European-Finnish (FIN) AF: 0.565 AC: 5963 AN: 10546

Middle Eastern (MID) AF: 0.590 AC: 171 AN: 290

European-Non Finnish (NFE) AF: 0.571 AC: 38717 AN: 67774

Other (OTH) AF: 0.576 AC: 1214 AN: 2106

Alfa AF: 0.561 Hom.: 3397

Bravo AF: 0.556

Asia WGS AF: 0.378 AC: 1316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.64
DANN	Benign	0.20
PhyloP100		0.064
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7585982; hg19: chr2-158975596;