rs17478556

chr1-84386440-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000471089.6(UOX):n.31-1629C>G 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 0.0295 in 152,312 control chromosomes in the GnomAD database, including 88 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 0.030 (88 hom., cov: 32)
• Consequence: UOX ENST00000471089.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.513

Genes affected

UOX (HGNC:12575): (urate oxidase (pseudogene)) Urate oxidase is an enzyme that catalyzes the oxidation of uric acid to allantoin. This gene has been inactivated by mutation and is nonfunctional in humans and some other primates. [provided by RefSeq, Jul 2008]

SAMD13 (HGNC:24582): (sterile alpha motif domain containing 13) Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in negative regulation of transcription, DNA-templated. Predicted to be active in nucleus. [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=-0.84).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0295 (4495/152312) while in subpopulation SAS AF= 0.0386 (186/4816). AF 95% confidence interval is 0.0341. There are 88 homozygotes in gnomad4. There are 2191 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 87 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UOX	ENST00000471089.6	n.31-1629C>G		intron_variant, non_coding_transcript_variant
SAMD13	ENST00000454967.1	c.70-1840G>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0295 AC: 4493 AN: 152194 Hom.: 87 Cov.: 32

Gnomad AFR AF: 0.0216

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0350

Gnomad ASJ AF: 0.0726

Gnomad EAS AF: 0.00982

Gnomad SAS AF: 0.0386

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0344

Gnomad OTH AF: 0.0315

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

GnomAD4 genome AF: 0.0295 AC: 4495 AN: 152312 Hom.: 88 Cov.: 32 AF XY: 0.0294 AC XY: 2191 AN XY: 74472

Gnomad4 AFR AF: 0.0216

Gnomad4 AMR AF: 0.0348

Gnomad4 ASJ AF: 0.0726

Gnomad4 EAS AF: 0.0100

Gnomad4 SAS AF: 0.0386

Gnomad4 FIN AF: 0.0127

Gnomad4 NFE AF: 0.0344

Gnomad4 OTH AF: 0.0312

Alfa AF: 0.0293 Hom.: 15

Bravo AF: 0.0302

Asia WGS AF: 0.0210 AC: 76 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.8
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17478556; hg19: chr1-84852123;