rs4628973

Positions:

• chr16-90045818-A-G

Variant summary

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

The NR_027335.2(URAHP):​n.228+1139T>C variant causes a intron, non coding transcript 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 NR_027335.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

Genes affected

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
URAHP	NR_027335.2	n.228+1139T>C		intron_variant, non_coding_transcript_variant
URAHP	NR_027336.2	n.181+1139T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
URAHP	ENST00000409873.5	n.228+1139T>C		intron_variant, non_coding_transcript_variant		1
URAHP	ENST00000517889.5	n.171+1139T>C		intron_variant, non_coding_transcript_variant		1
URAHP	ENST00000610227.1	n.200+1139T>C		intron_variant, non_coding_transcript_variant
URAHP	ENST00000521551.5	n.234+1139T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.370

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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