rs2287839

Positions:

• chr19-9830138-C-G

Variant summary

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

The variant allele was found at a frequency of 0.0823 in 1,199,304 control chromosomes in the GnomAD database, including 6,708 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 0.14 (2368 hom., cov: 32)
  • Exomes 𝑓: 0.074 (4340 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620

Genes affected

(HGNC:):

UBL5 (HGNC:13736): (ubiquitin like 5) This gene encodes a member of a group of proteins similar to ubiquitin. The encoded protein is not thought to degrade proteins like ubiquitin but to affect their function through being bound to target proteins by an isopeptide bond. The gene product has been studied as a link to predisposition to obesity based on its expression in Psammomys obesus, the fat sand rat, which is an animal model for obesity studies. Variation in this gene was found to be significantly associated with some metabolic traits (PMID: 15331561) but not associated with childhood obesity (PMID: 19189687). Pseudogenes of this gene are located on chromosomes 3, 5 and 17. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jan 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.9830138C>G		intergenic_region
UBL5	NM_001048241.3	c.*130C>G		downstream_gene_variant		ENST00000586895.6	NP_001041706.1
UBL5	NM_024292.4	c.*130C>G		downstream_gene_variant			NP_077268.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBL5	ENST00000586895.6	c.*130C>G		downstream_gene_variant		1	NM_001048241.3	ENSP00000468656.1
UBL5	ENST00000593087.1	c.*153C>G		downstream_gene_variant		3		ENSP00000467663.1

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20827 AN: 152050 Hom.: 2358 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.0978

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0438

Gnomad EAS AF: 0.0494

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0574

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0638

Gnomad OTH AF: 0.131

GnomAD4 exome AF: 0.0743 AC: 77764 AN: 1047134 Hom.: 4340 Cov.: 13 AF XY: 0.0758 AC XY: 40048 AN XY: 528294

Gnomad4 AFR exome AF: 0.307

Gnomad4 AMR exome AF: 0.134

Gnomad4 ASJ exome AF: 0.0465

Gnomad4 EAS exome AF: 0.0442

Gnomad4 SAS exome AF: 0.161

Gnomad4 FIN exome AF: 0.0523

Gnomad4 NFE exome AF: 0.0588

Gnomad4 OTH exome AF: 0.0858

GnomAD4 genome AF: 0.137 AC: 20886 AN: 152170 Hom.: 2368 Cov.: 32 AF XY: 0.137 AC XY: 10181 AN XY: 74392

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.0438

Gnomad4 EAS AF: 0.0494

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.0574

Gnomad4 NFE AF: 0.0638

Gnomad4 OTH AF: 0.133

Alfa AF: 0.108 Hom.: 205

Bravo AF: 0.148

Asia WGS AF: 0.160 AC: 557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2287839; hg19: chr19-9940814;