rs6737672

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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=-0.82).
• 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
UPP2	ENST00000489438.2	n.-20+53641G>A		intron_variant	Intron 1 of 9	3		ENSP00000520425.1

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

African (AFR) AF: 0.121 AC: 5005 AN: 41486

American (AMR) AF: 0.619 AC: 9438 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2030 AN: 3468

East Asian (EAS) AF: 0.616 AC: 3181 AN: 5166

South Asian (SAS) AF: 0.613 AC: 2949 AN: 4808

European-Finnish (FIN) AF: 0.484 AC: 5109 AN: 10546

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32564 AN: 67942

Other (OTH) AF: 0.455 AC: 959 AN: 2106

Alfa AF: 0.471 Hom.: 30109

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
PhyloP100		-0.58
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6737672; hg19: chr2-158786869; COSMIC: COSV107554273;