2-158107775-A-G

Variant names:

• chr2-158107775-A-G
• rs6437133
• NM_173355.4:c.180+1559A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173355.4(UPP2):​c.180+1559A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,934 control chromosomes in the GnomAD database, including 23,057 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 0.54 (23057 hom., cov: 31)
• Consequence: UPP2 NM_173355.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154
• Publications: 4 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 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.180+1559A>G		intron	N/A	NP_775491.1
	UPP2	NM_001135098.2		c.351+1559A>G		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.180+1559A>G		intron	N/A	ENSP00000005756.5
	UPP2	ENST00000605860.5	TSL:5	c.351+1559A>G		intron	N/A	ENSP00000474090.1
	UPP2	ENST00000460456.1	TSL:5	n.376+1559A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81985 AN: 151816 Hom.: 23043 Cov.: 31

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.0567

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.540 AC: 82044 AN: 151934 Hom.: 23057 Cov.: 31 AF XY: 0.534 AC XY: 39643 AN XY: 74236

African (AFR) AF: 0.607 AC: 25158 AN: 41446

American (AMR) AF: 0.537 AC: 8195 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1716 AN: 3468

East Asian (EAS) AF: 0.0564 AC: 291 AN: 5160

South Asian (SAS) AF: 0.384 AC: 1847 AN: 4816

European-Finnish (FIN) AF: 0.552 AC: 5827 AN: 10556

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37127 AN: 67916

Other (OTH) AF: 0.565 AC: 1186 AN: 2100

Alfa AF: 0.537 Hom.: 10860

Bravo AF: 0.545

Asia WGS AF: 0.291 AC: 1014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.58
PhyloP100		-0.15
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: rs6437133; hg19: chr2-158964287;