chr2-157935048-A-G

Variant names:

• chr2-157935048-A-G
• rs6720264
• ENST00000605860.5:c.-20+58320A>G

Variant summary

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

The ENST00000605860.5(UPP2):​c.-20+58320A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 151,852 control chromosomes in the GnomAD database, including 35,063 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 0.67 (35063 hom., cov: 30)
• Consequence: UPP2 ENST00000605860.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UPP2	ENST00000605860.5	c.-20+58320A>G		intron_variant	Intron 1 of 9	5		ENSP00000474090.1

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101099 AN: 151734 Hom.: 35052 Cov.: 30

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.666 AC: 101154 AN: 151852 Hom.: 35063 Cov.: 30 AF XY: 0.673 AC XY: 49903 AN XY: 74204

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.790

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.953

Gnomad4 SAS AF: 0.785

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.691

Alfa AF: 0.707 Hom.: 79772

Bravo AF: 0.662

Asia WGS AF: 0.835 AC: 2903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6720264; hg19: chr2-158791560;