rs6737672

Variant names:

• chr2-157930357-G-A
• rs6737672
• ENST00000605860.5:c.-20+53629G>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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UPP2	ENST00000605860.5	c.-20+53629G>A		intron_variant	Intron 1 of 9	5		ENSP00000474090.1

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;