Variant 7-48107042-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_003364.4(UPP1):c.606A>G(p.Thr202Thr) 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

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -4.04

Variant links:

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]

UPP1 links:

UPP1 (HGNC:):

UPP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 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_multiple_submitters_no_conflicts, 2 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	Protein	UniProt
UPP1	NM_003364.4 linkuse as main transcript	c.606A>G	p.Thr202Thr	synonymous_variant	7/9	ENST00000395564.9	NP_003355.1	Q16831-1B4DND0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UPP1	ENST00000395564.9 linkuse as main transcript	c.606A>G	p.Thr202Thr	synonymous_variant	7/9	1	NM_003364.4	ENSP00000378931.4		Q16831-1

Frequencies

GnomAD3 genomes

AF:

0.0266

AC:

4043

AN:

152172

Hom.:

169

Cov.:

show subpopulations

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.:

AF XY:

0.00619

AC XY:

841

AN XY:

135818

show subpopulations

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.:

AF XY:

0.00317

AC XY:

2299

AN XY:

726336

show subpopulations

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.:

AF XY:

0.0249

AC XY:

1853

AN XY:

74454

show subpopulations

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.:

Bravo

AF:

0.0298

Asia WGS

AF:

0.00404

AC:

AN:

3478

EpiCase

AF:

0.00196

EpiControl

AF:

0.00267

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Aug 08, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over