2-158094571-A-G

Variant names:

• chr2-158094571-A-G
• rs6437129
• NM_001135098.2:c.148-7469A>G

Variant summary

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001135098.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UPP2	NM_001135098.2		c.148-7469A>G		intron	N/A	NP_001128570.1	O95045-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UPP2	ENST00000605860.5	TSL:5	c.148-7469A>G		intron	N/A	ENSP00000474090.1	O95045-2
	UPP2	ENST00000890004.1		c.-24-7469A>G		intron	N/A	ENSP00000560063.1
	UPP2	ENST00000489438.2	TSL:3	n.148-11528A>G		intron	N/A	ENSP00000520425.1	A0AAQ5BIC7

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

African (AFR) AF: 0.770 AC: 31939 AN: 41486

American (AMR) AF: 0.684 AC: 10456 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2362 AN: 3472

East Asian (EAS) AF: 0.467 AC: 2402 AN: 5148

South Asian (SAS) AF: 0.540 AC: 2591 AN: 4800

European-Finnish (FIN) AF: 0.678 AC: 7177 AN: 10578

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48560 AN: 67976

Other (OTH) AF: 0.728 AC: 1539 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	13
DANN	Benign	0.70
PhyloP100		0.085
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: rs6437129; hg19: chr2-158951083;