rs6737672

Positions:

• chr2-157930357-G-A

Variant summary

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

The ENST00000605860.5(UPP2):​c.-20+53629G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,980 control chromosomes in the GnomAD database, including 15,331 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 0.41 (15331 hom., cov: 31)
• Consequence: UPP2 ENST00000605860.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UPP2	ENST00000605860.5	c.-20+53629G>A		intron_variant		5		ENSP00000474090

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61833 AN: 151862 Hom.: 15329 Cov.: 31

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.407 AC: 61829 AN: 151980 Hom.: 15331 Cov.: 31 AF XY: 0.416 AC XY: 30863 AN XY: 74278

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.455

Alfa AF: 0.479 Hom.: 24241

Bravo AF: 0.403

Asia WGS AF: 0.570 AC: 1983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.91
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6737672; hg19: chr2-158786869;