rs4404222

Variant names:

• chr2-157886996-G-A
• rs4404222
• ENST00000605860.5:c.-20+10268G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-157886996-G-A
• chr2-157886996-G-C

Variant summary

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

The ENST00000890004.1(UPP2):​c.-191+10268G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 147,408 control chromosomes in the GnomAD database, including 2,166 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 0.14 (2166 hom., cov: 27)
• Consequence: UPP2 ENST00000890004.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578
• Publications: 3 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]

LOC105373714 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000890004.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UPP2	ENST00000605860.5	TSL:5	c.-20+10268G>A		intron	N/A	ENSP00000474090.1	O95045-2
	UPP2	ENST00000890004.1		c.-191+10268G>A		intron	N/A	ENSP00000560063.1
	UPP2	ENST00000489438.2	TSL:3	n.-20+10280G>A		intron	N/A	ENSP00000520425.1	A0AAQ5BIC7

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21086 AN: 147370 Hom.: 2165 Cov.: 27

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.0873

Gnomad ASJ AF: 0.0921

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0814

Gnomad MID AF: 0.0839

Gnomad NFE AF: 0.0800

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.143 AC: 21101 AN: 147408 Hom.: 2166 Cov.: 27 AF XY: 0.144 AC XY: 10338 AN XY: 71590

African (AFR) AF: 0.261 AC: 10405 AN: 39824

American (AMR) AF: 0.0872 AC: 1289 AN: 14778

Ashkenazi Jewish (ASJ) AF: 0.0921 AC: 318 AN: 3452

East Asian (EAS) AF: 0.359 AC: 1781 AN: 4962

South Asian (SAS) AF: 0.154 AC: 719 AN: 4682

European-Finnish (FIN) AF: 0.0814 AC: 738 AN: 9062

Middle Eastern (MID) AF: 0.0880 AC: 25 AN: 284

European-Non Finnish (NFE) AF: 0.0800 AC: 5391 AN: 67410

Other (OTH) AF: 0.134 AC: 274 AN: 2048

Alfa AF: 0.119 Hom.: 1455

Bravo AF: 0.153

Asia WGS AF: 0.278 AC: 961 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.25
PhyloP100		-0.58
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

dbSNP: rs4404222;

hg19: chr2-158743508;