rs869048

Variant names:

• chr16-90046540-G-A
• rs869048
• ENST00000409873.5:n.228+417C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-90046540-G-A
• chr16-90046540-G-C

Variant summary

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

The ENST00000409873.5(URAHP):​n.228+417C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,970 control chromosomes in the GnomAD database, including 20,399 homozygotes. 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 0.48 (20399 hom., cov: 32)
• Consequence: URAHP ENST00000409873.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.555
• Publications: 4 publications found

Genes affected

URAHP (HGNC:):

URAHP (HGNC:43695): (urate (hydroxyiso-) hydrolase, pseudogene) Predicted to enable hydroxyisourate hydrolase activity. Predicted to be involved in allantoin metabolic process; purine-containing compound catabolic process; and urate catabolic process. Predicted to be active in peroxisome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000409873.5. 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
	URAHP	NR_027335.2		n.228+417C>T		intron	N/A
	URAHP	NR_027336.2		n.181+417C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	URAHP	ENST00000409873.5	TSL:1	n.228+417C>T		intron	N/A
	URAHP	ENST00000517889.6	TSL:1	n.203+417C>T		intron	N/A
	URAHP	ENST00000409768.3	TSL:3	n.202+417C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72868 AN: 151852 Hom.: 20339 Cov.: 32

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.480 AC: 72988 AN: 151970 Hom.: 20399 Cov.: 32 AF XY: 0.487 AC XY: 36190 AN XY: 74260

African (AFR) AF: 0.745 AC: 30855 AN: 41432

American (AMR) AF: 0.490 AC: 7482 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 974 AN: 3472

East Asian (EAS) AF: 0.794 AC: 4101 AN: 5162

South Asian (SAS) AF: 0.387 AC: 1866 AN: 4820

European-Finnish (FIN) AF: 0.506 AC: 5356 AN: 10582

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21227 AN: 67912

Other (OTH) AF: 0.401 AC: 845 AN: 2106

Alfa AF: 0.359 Hom.: 14513

Bravo AF: 0.496

Asia WGS AF: 0.607 AC: 2112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.48
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs869048; hg19: chr16-90112948;