rs307682

chr9-33973326-A-G

Variant summary

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

The NM_001370062.2(UBAP2):c.521-89T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 1,371,526 control chromosomes in the GnomAD database, including 25,101 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 0.19 (2936 hom., cov: 32)
  • Exomes 𝑓: 0.18 (22165 hom.)
• Consequence: UBAP2 NM_001370062.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.80

Genes affected

UBAP2 (HGNC:14185): (ubiquitin associated protein 2) The protein encoded by this gene contains a UBA (ubiquitin associated) domain, which is characteristic of proteins that function in the ubiquitination pathway. This gene may show increased expression in the adrenal gland and lymphatic tissues. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBAP2	NM_001370062.2	c.521-89T>C		intron_variant		ENST00000379238.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBAP2	ENST00000379238.7	c.521-89T>C		intron_variant		5	NM_001370062.2	P2

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29206 AN: 151962 Hom.: 2930 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.183

GnomAD4 exome AF: 0.181 AC: 221279 AN: 1219446 Hom.: 22165 AF XY: 0.187 AC XY: 115708 AN XY: 617368

Gnomad4 AFR exome AF: 0.231

Gnomad4 AMR exome AF: 0.144

Gnomad4 ASJ exome AF: 0.151

Gnomad4 EAS exome AF: 0.222

Gnomad4 SAS exome AF: 0.347

Gnomad4 FIN exome AF: 0.195

Gnomad4 NFE exome AF: 0.165

Gnomad4 OTH exome AF: 0.183

GnomAD4 genome AF: 0.192 AC: 29243 AN: 152080 Hom.: 2936 Cov.: 32 AF XY: 0.195 AC XY: 14517 AN XY: 74358

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.185

Alfa AF: 0.183 Hom.: 1358

Bravo AF: 0.185

Asia WGS AF: 0.269 AC: 938 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	9.3
Dann	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs307682; hg19: chr9-33973324; COSMIC: COSV62545148; COSMIC: COSV62545148;