chr7-48102597-G-T

Variant names:

• chr7-48102597-G-T
• rs6463462
• NM_003364.4:c.321+615G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003364.4(UPP1):​c.321+615G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 151,970 control chromosomes in the GnomAD database, including 26,822 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 0.59 (26822 hom., cov: 31)
• Consequence: UPP1 NM_003364.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 6 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UPP1	NM_003364.4	c.321+615G>T		intron_variant	Intron 5 of 8	ENST00000395564.9	NP_003355.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UPP1	ENST00000395564.9	c.321+615G>T		intron_variant	Intron 5 of 8	1	NM_003364.4	ENSP00000378931.4

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90053 AN: 151852 Hom.: 26792 Cov.: 31

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.625

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.593 AC: 90134 AN: 151970 Hom.: 26822 Cov.: 31 AF XY: 0.594 AC XY: 44132 AN XY: 74264

African (AFR) AF: 0.595 AC: 24670 AN: 41428

American (AMR) AF: 0.600 AC: 9170 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2253 AN: 3470

East Asian (EAS) AF: 0.550 AC: 2842 AN: 5166

South Asian (SAS) AF: 0.658 AC: 3170 AN: 4818

European-Finnish (FIN) AF: 0.593 AC: 6252 AN: 10550

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39735 AN: 67948

Other (OTH) AF: 0.628 AC: 1324 AN: 2108

Alfa AF: 0.592 Hom.: 111694

Bravo AF: 0.592

Asia WGS AF: 0.580 AC: 2014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.27
DANN	Benign	0.52
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6463462; hg19: chr7-48142194;