Genetic Variant UPP2:c.-25_-24insA (chr2-158102039-G-GA) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_173355.4(UPP2):c.-25_-24insA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0447 in 1,610,214 control chromosomes in the GnomAD database, including 4,457 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.10 ( 1596 hom., cov: 31)

Exomes 𝑓: 0.039 ( 2861 hom. )

Consequence

UPP2
NM_173355.4 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.801

Publications

6 publications found

Variant links:

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]

UPP2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein
UPP2	NM_173355.4 link	c.-25_-24insA		5_prime_UTR_variant	Exon 1 of 7	ENST00000005756.5	NP_775491.1
UPP2	NM_001135098.2 link	c.148-1_148insA	p.Val50fs	frameshift_variant, splice_region_variant	Exon 3 of 9		NP_001128570.1
UPP2	XM_017003484.2 link	c.-25_-24insA		5_prime_UTR_variant	Exon 1 of 6		XP_016858973.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UPP2	ENST00000005756.5 link	c.-25_-24insA		5_prime_UTR_variant	Exon 1 of 7	1	NM_173355.4	ENSP00000005756.5		O95045-1

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15637

AN:

152012

Hom.:

1578

Cov.:

show subpopulations

Gnomad AFR

AF:

0.262

Gnomad AMI

AF:

0.0406

Gnomad AMR

AF:

0.0570

Gnomad ASJ

AF:

0.0781

Gnomad EAS

AF:

0.142

Gnomad SAS

AF:

0.110

Gnomad FIN

AF:

0.0212

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.0278

Gnomad OTH

AF:

0.0953

GnomAD2 exomes

AF:

0.0632

AC:

15755

AN:

249272

AF XY:

0.0616

show subpopulations

Gnomad AFR exome

AF:

0.268

Gnomad AMR exome

AF:

0.0289

Gnomad ASJ exome

AF:

0.0726

Gnomad EAS exome

AF:

0.133

Gnomad FIN exome

AF:

0.0188

Gnomad NFE exome

AF:

0.0300

Gnomad OTH exome

AF:

0.0489

GnomAD4 exome

AF:

0.0386

AC:

56351

AN:

1458084

Hom.:

2861

Cov.:

AF XY:

0.0401

AC XY:

29081

AN XY:

725346

show subpopulations

African (AFR)

AF:

0.277

AC:

9141

AN:

33048

American (AMR)

AF:

0.0333

AC:

1482

AN:

44460

Ashkenazi Jewish (ASJ)

AF:

0.0697

AC:

1814

AN:

26038

East Asian (EAS)

AF:

0.118

AC:

4676

AN:

39522

South Asian (SAS)

AF:

0.104

AC:

8909

AN:

85508

European-Finnish (FIN)

AF:

0.0195

AC:

1039

AN:

53268

Middle Eastern (MID)

AF:

0.110

AC:

631

AN:

5732

European-Non Finnish (NFE)

AF:

0.0227

AC:

25207

AN:

1110302

Other (OTH)

AF:

0.0573

AC:

3452

AN:

60206

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.414

Heterozygous variant carriers

2329

4658

6988

9317

11646

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1136

2272

3408

4544

5680

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.103

AC:

15700

AN:

152130

Hom.:

1596

Cov.:

AF XY:

0.103

AC XY:

7626

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.263

AC:

10905

AN:

41446

American (AMR)

AF:

0.0569

AC:

870

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0781

AC:

271

AN:

3470

East Asian (EAS)

AF:

0.142

AC:

733

AN:

5166

South Asian (SAS)

AF:

0.110

AC:

533

AN:

4828

European-Finnish (FIN)

AF:

0.0212

AC:

225

AN:

10596

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0278

AC:

1888

AN:

68012

Other (OTH)

AF:

0.0967

AC:

204

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

632

1263

1895

2526

3158

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

162

324

486

648

810

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0457

Hom.:

246

Bravo

AF:

0.113

Asia WGS

AF:

0.143

AC:

497

AN:

3478

EpiCase

AF:

0.0335

EpiControl

AF:

0.0355

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.80

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over