rs7886499

Variant names:

• chrX-75286551-A-G
• rs7886499
• NM_145052.4:c.387-6921A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The NM_145052.4(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 NM_145052.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495
• Publications: 0 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=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UPRT	NM_145052.4	c.387-6921A>G		intron_variant	Intron 1 of 6	ENST00000373383.9	NP_659489.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UPRT	ENST00000373383.9	c.387-6921A>G		intron_variant	Intron 1 of 6	1	NM_145052.4	ENSP00000362481.4

Frequencies

GnomAD3 genomes AF: 0.832 AC: 92231 AN: 110893 Hom.: 28483 Cov.: 23

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

African (AFR) AF: 0.486 AC: 14765 AN: 30403

American (AMR) AF: 0.929 AC: 9670 AN: 10412

Ashkenazi Jewish (ASJ) AF: 0.970 AC: 2564 AN: 2642

East Asian (EAS) AF: 0.976 AC: 3447 AN: 3532

South Asian (SAS) AF: 0.861 AC: 2268 AN: 2634

European-Finnish (FIN) AF: 0.983 AC: 5830 AN: 5931

Middle Eastern (MID) AF: 0.948 AC: 199 AN: 210

European-Non Finnish (NFE) AF: 0.972 AC: 51504 AN: 53005

Other (OTH) AF: 0.871 AC: 1299 AN: 1492

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
PhyloP100		-0.49
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: rs7886499; hg19: chrX-74506386;