chr13-27978330-C-A

Variant names:

• chr13-27978330-C-A
• rs1354727253
• NM_001105577.2:c.298G>T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001105577.2(URAD):​c.298G>T​(p.Glu100*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: URAD NM_001105577.2 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.85
• Publications: 0 publications found

Genes affected

URAD (HGNC:17785): (ureidoimidazoline (2-oxo-4-hydroxy-4-carboxy-5-) decarboxylase) Predicted to enable carboxy-lyase activity. Predicted to be involved in purine-containing compound catabolic process. Predicted to be active in peroxisome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001105577.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	URAD	NM_001105577.2	MANE Select	c.298G>T	p.Glu100*	stop_gained	Exon 2 of 2	NP_001099047.1	A6NGE7
	URAD	NR_197241.1		n.183G>T		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	URAD	ENST00000332715.6	TSL:5 MANE Select	c.298G>T	p.Glu100*	stop_gained	Exon 2 of 2	ENSP00000333490.4	A6NGE7
	URAD	ENST00000713555.1		n.289G>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1241742 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 605252

African (AFR) AF: 0.00 AC: 0 AN: 24356

American (AMR) AF: 0.00 AC: 0 AN: 13212

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18728

East Asian (EAS) AF: 0.00 AC: 0 AN: 27296

South Asian (SAS) AF: 0.00 AC: 0 AN: 58164

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30556

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4286

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1013896

Other (OTH) AF: 0.00 AC: 0 AN: 51248

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.52	D
BayesDel_noAF	Pathogenic	0.51
CADD	Pathogenic	36
DANN	Uncertain	1.0
Eigen	Pathogenic	0.80
Eigen_PC	Uncertain	0.55
FATHMM_MKL	Pathogenic	0.97	D
PhyloP100		2.9
Vest4		0.45
GERP RS		4.7
Mutation Taster		=120/80	polymorphism

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: rs1354727253; hg19: chr13-28552467;