X-75235243-G-C

Position:

• chrX-75235243-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007068269.1(LOC124905200):​n.560-9678C>G variant causes a intron, non coding transcript 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: LOC124905200 XR_007068269.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

LOC124905200 (HGNC:):

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 Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124905200	XR_007068269.1	n.560-9678C>G		intron_variant, non_coding_transcript_variant
UPRT	NM_001363821.1	c.-23+11618G>C		intron_variant
LOC124905200	XR_007068268.1	n.560-9678C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UPRT	ENST00000652605.1	c.-446-55781G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0759 AC: 8447 AN: 111338 Hom.: 1238 Cov.: 22 AF XY: 0.0858 AC XY: 2879 AN XY: 33544

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

Gnomad4 AFR AF: 0.0129

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.0390

Gnomad4 EAS AF: 0.893

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.0512

Gnomad4 NFE AF: 0.0281

Gnomad4 OTH AF: 0.0790

Alfa AF: 0.0491 Hom.: 290

Bravo AF: 0.0957

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs6647668; hg19: chrX-74455078;