16-90045818-A-G

Variant names:

• chr16-90045818-A-G
• rs4628973
• ENST00000409873.5:n.228+1139T>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+1139T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,320 control chromosomes in the GnomAD database, including 18,370 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 0.46 (18370 hom., cov: 31)
• Consequence: URAHP ENST00000409873.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 2 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 = 0.771 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	URAHP	NR_027335.2		n.228+1139T>C		intron	N/A
	URAHP	NR_027336.2		n.181+1139T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	URAHP	ENST00000409873.5	TSL:1	n.228+1139T>C		intron	N/A
	URAHP	ENST00000517889.6	TSL:1	n.203+1139T>C		intron	N/A
	URAHP	ENST00000409768.3	TSL:3	n.202+1139T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.455 AC: 68841 AN: 151202 Hom.: 18316 Cov.: 31

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.214

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.456 AC: 68955 AN: 151320 Hom.: 18370 Cov.: 31 AF XY: 0.464 AC XY: 34334 AN XY: 73920

African (AFR) AF: 0.705 AC: 29100 AN: 41254

American (AMR) AF: 0.472 AC: 7176 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 865 AN: 3462

East Asian (EAS) AF: 0.792 AC: 4056 AN: 5124

South Asian (SAS) AF: 0.388 AC: 1853 AN: 4770

European-Finnish (FIN) AF: 0.495 AC: 5185 AN: 10468

Middle Eastern (MID) AF: 0.220 AC: 63 AN: 286

European-Non Finnish (NFE) AF: 0.291 AC: 19700 AN: 67752

Other (OTH) AF: 0.370 AC: 776 AN: 2098

Alfa AF: 0.370 Hom.: 2629

Bravo AF: 0.470

Asia WGS AF: 0.600 AC: 2089 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.80
DANN	Benign	0.095
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs4628973; hg19: chr16-90112226; COSMIC: COSV51946484;