rs12832571

Variant names:

• chrX-75298324-G-A
• rs12832571
• NM_145052.4:c.562+771G>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_145052.4(UPRT):​c.562+771G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.68 (21368 hom., 21150 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: UPRT NM_145052.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.814
• Publications: 2 publications found

Genes affected

UPRT (HGNC:28334): (uracil phosphoribosyltransferase homolog) This gene encodes uracil phosphoribosyltransferase, which catalyzes the conversion of uracil and 5-phosphoribosyl-1-R-diphosphate to uridine monophosphate (UMP). This reaction is an important part of nucleotide metabolism, specifically the pyrimidine salvage pathway. The enzyme localizes to the nucleus and cytoplasm. The protein is a potential target for rational design of drugs to treat parasitic infections and cancer. [provided by RefSeq, Nov 2009]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UPRT	NM_145052.4	c.562+771G>A		intron_variant	Intron 4 of 6	ENST00000373383.9	NP_659489.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UPRT	ENST00000373383.9	c.562+771G>A		intron_variant	Intron 4 of 6	1	NM_145052.4	ENSP00000362481.4

Frequencies

GnomAD3 genomes AF: 0.683 AC: 74300 AN: 108814 Hom.: 21384 Cov.: 21

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.982

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.875

Gnomad NFE AF: 0.907

Gnomad OTH AF: 0.730

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.682 AC: 74280 AN: 108867 Hom.: 21368 Cov.: 21 AF XY: 0.677 AC XY: 21150 AN XY: 31219

African (AFR) AF: 0.301 AC: 9034 AN: 29966

American (AMR) AF: 0.664 AC: 6700 AN: 10092

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 2329 AN: 2611

East Asian (EAS) AF: 0.117 AC: 400 AN: 3408

South Asian (SAS) AF: 0.522 AC: 1285 AN: 2464

European-Finnish (FIN) AF: 0.912 AC: 5081 AN: 5573

Middle Eastern (MID) AF: 0.872 AC: 184 AN: 211

European-Non Finnish (NFE) AF: 0.907 AC: 47542 AN: 52396

Other (OTH) AF: 0.722 AC: 1064 AN: 1473

Alfa AF: 0.823 Hom.: 94969

Bravo AF: 0.645

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.8
DANN	Benign	0.69
PhyloP100		0.81
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: rs12832571; hg19: chrX-74518159;