rs7886499

Positions:

• chrX-75286551-A-G
• chrX-75286551-A-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000373383.9(UPRT):​c.387-6921A>G 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 0.83 (28469 hom., 27889 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: UPRT ENST00000373383.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495

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

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UPRT	NM_145052.4	c.387-6921A>G		intron_variant		ENST00000373383.9	NP_659489.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UPRT	ENST00000373383.9	c.387-6921A>G		intron_variant		1	NM_145052.4	ENSP00000362481	P1

Frequencies

GnomAD3 genomes AF: 0.832 AC: 92231 AN: 110893 Hom.: 28483 Cov.: 23 AF XY: 0.842 AC XY: 27869 AN XY: 33105

Gnomad AFR AF: 0.486

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.929

Gnomad ASJ AF: 0.970

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.952

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.870

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: 0.831 AC: 92229 AN: 110944 Hom.: 28469 Cov.: 23 AF XY: 0.841 AC XY: 27889 AN XY: 33166

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.929

Gnomad4 ASJ AF: 0.970

Gnomad4 EAS AF: 0.976

Gnomad4 SAS AF: 0.861

Gnomad4 FIN AF: 0.983

Gnomad4 NFE AF: 0.972

Gnomad4 OTH AF: 0.871

Alfa AF: 0.916 Hom.: 13157

Bravo AF: 0.815

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.13
DANN	Benign	0.36

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

Other links and lift over

dbSNP: rs7886499; hg19: chrX-74506386;