X-75235243-G-C

Variant names:

• chrX-75235243-G-C
• rs6647668
• NM_001363821.1:c.-23+11618G>C

Variant summary

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

The NM_001363821.1(UPRT):​c.-23+11618G>C variant causes a intron change. The variant allele was found at a frequency of 0.0758 in 111,391 control chromosomes in the GnomAD database, including 1,236 homozygotes. There are 2,880 hemizygotes in GnomAD. 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 0.076 (1236 hom., 2880 hem., cov: 22)
• Consequence: UPRT NM_001363821.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• 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]

LOC124905200 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001363821.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UPRT	NM_001363821.1		c.-23+11618G>C		intron	N/A	NP_001350750.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UPRT	ENST00000652605.1		c.-446-55781G>C		intron	N/A	ENSP00000498525.1

Frequencies

GnomAD3 genomes AF: 0.0759 AC: 8447 AN: 111338 Hom.: 1238 Cov.: 22

Gnomad AFR AF: 0.0130

Gnomad AMI AF: 0.00875

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.0390

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.0512

Gnomad MID AF: 0.0126

Gnomad NFE AF: 0.0281

Gnomad OTH AF: 0.0734

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

GnomAD4 genome AF: 0.0758 AC: 8446 AN: 111391 Hom.: 1236 Cov.: 22 AF XY: 0.0857 AC XY: 2880 AN XY: 33607

African (AFR) AF: 0.0129 AC: 397 AN: 30686

American (AMR) AF: 0.217 AC: 2272 AN: 10458

Ashkenazi Jewish (ASJ) AF: 0.0390 AC: 103 AN: 2641

East Asian (EAS) AF: 0.893 AC: 3077 AN: 3446

South Asian (SAS) AF: 0.257 AC: 671 AN: 2611

European-Finnish (FIN) AF: 0.0512 AC: 308 AN: 6018

Middle Eastern (MID) AF: 0.00922 AC: 2 AN: 217

European-Non Finnish (NFE) AF: 0.0281 AC: 1490 AN: 53109

Other (OTH) AF: 0.0790 AC: 120 AN: 1519

Alfa AF: 0.0491 Hom.: 290

Bravo AF: 0.0957

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.88
DANN	Benign	0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6647668; hg19: chrX-74455078;