7-48107042-A-C

Variant names:

• chr7-48107042-A-C
• NM_003364.4:c.606A>C
• UPP1 p.Thr202Thr

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_003364.4(UPP1):​c.606A>C​(p.Thr202Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. T202T) has been classified as Benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: UPP1 NM_003364.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.04
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BP7: Synonymous conserved (PhyloP=-4.04 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003364.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UPP1	NM_003364.4	MANE Select	c.606A>C	p.Thr202Thr	synonymous	Exon 7 of 9	NP_003355.1	Q16831-1
	UPP1	NM_001287426.2		c.606A>C	p.Thr202Thr	synonymous	Exon 8 of 10	NP_001274355.1	Q16831-1
	UPP1	NM_001362774.2		c.606A>C	p.Thr202Thr	synonymous	Exon 8 of 10	NP_001349703.1	Q16831-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UPP1	ENST00000395564.9	TSL:1 MANE Select	c.606A>C	p.Thr202Thr	synonymous	Exon 7 of 9	ENSP00000378931.4	Q16831-1
	UPP1	ENST00000331803.8	TSL:1	c.606A>C	p.Thr202Thr	synonymous	Exon 8 of 10	ENSP00000330032.4	Q16831-1
	UPP1	ENST00000417464.6	TSL:1	n.*103A>C		non_coding_transcript_exon	Exon 4 of 6	ENSP00000413611.2	Q16831-2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0060
DANN	Benign	0.32
PhyloP100		-4.0

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr7-48146639;