7-48107042-A-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_Strong BP6_Moderate BP7 BA1

The NM_003364.4(UPP1):c.606A>G(p.Thr202=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00574 in 1,612,346 control chromosomes in the GnomAD database, including 343 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.027 (169 hom., cov: 33)
  • Exomes 𝑓: 0.0036 (174 hom.)
• Consequence: UPP1 NM_003364.4 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.04

Genes affected

UPP1 (HGNC:12576): (uridine phosphorylase 1) This gene encodes a uridine phosphorylase, an enzyme that catalyzes the reversible phosphorylation of uridine (or 2'- deoxyuridine) to uracil and ribose-1-phosphate (or deoxyribose-1-phosphate). The encoded enzyme functions in the degradation and salvage of pyrimidine ribonucleosides. [provided by RefSeq, Oct 2016]

ACMG classification

Verdict is Benign. Variant got -15 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BP6: Variant 7-48107042-A-G is Benign according to our data. Variant chr7-48107042-A-G is described in ClinVar as [Benign]. Clinvar id is 769712.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-4.04 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UPP1	NM_003364.4	c.606A>G	p.Thr202=	synonymous_variant	7/9	ENST00000395564.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UPP1	ENST00000395564.9	c.606A>G	p.Thr202=	synonymous_variant	7/9	1	NM_003364.4	P1

Frequencies

GnomAD3 genomes AF: 0.0266 AC: 4043 AN: 152172 Hom.: 169 Cov.: 33

Gnomad AFR AF: 0.0903

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00850

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00166

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00143

Gnomad OTH AF: 0.0196

GnomAD3 exomes AF: 0.00772 AC: 1939 AN: 251296 Hom.: 68 AF XY: 0.00619 AC XY: 841 AN XY: 135818

Gnomad AFR exome AF: 0.0906

Gnomad AMR exome AF: 0.00503

Gnomad ASJ exome AF: 0.00466

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.000849

Gnomad FIN exome AF: 0.0000463

Gnomad NFE exome AF: 0.00158

Gnomad OTH exome AF: 0.00620

GnomAD4 exome AF: 0.00356 AC: 5205 AN: 1460056 Hom.: 174 Cov.: 30 AF XY: 0.00317 AC XY: 2299 AN XY: 726336

Gnomad4 AFR exome AF: 0.0962

Gnomad4 AMR exome AF: 0.00581

Gnomad4 ASJ exome AF: 0.00497

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000894

Gnomad4 FIN exome AF: 0.0000937

Gnomad4 NFE exome AF: 0.000884

Gnomad4 OTH exome AF: 0.00774

GnomAD4 genome AF: 0.0266 AC: 4050 AN: 152290 Hom.: 169 Cov.: 33 AF XY: 0.0249 AC XY: 1853 AN XY: 74454

Gnomad4 AFR AF: 0.0902

Gnomad4 AMR AF: 0.00849

Gnomad4 ASJ AF: 0.00634

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00166

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00143

Gnomad4 OTH AF: 0.0194

Alfa AF: 0.00812 Hom.: 45

Bravo AF: 0.0298

Asia WGS AF: 0.00404 AC: 14 AN: 3478

EpiCase AF: 0.00196

EpiControl AF: 0.00267

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Aug 08, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.0070
Dann	Benign	0.29

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

LitVar

Other links and lift over

dbSNP: rs2230761; hg19: chr7-48146639;