rs307682

Variant names:

• chr9-33973326-A-G
• rs307682
• NM_001370062.2:c.521-89T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000379238.7(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 ENST00000379238.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.80
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000379238.7. 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
	UBAP2	NM_001370062.2	MANE Select	c.521-89T>C		intron	N/A	NP_001356991.2
	UBAP2	NM_001370059.2		c.521-89T>C		intron	N/A	NP_001356988.2
	UBAP2	NM_018449.4		c.521-89T>C		intron	N/A	NP_060919.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBAP2	ENST00000379238.7	TSL:5 MANE Select	c.521-89T>C		intron	N/A	ENSP00000368540.2
	UBAP2	ENST00000682239.1		c.521-89T>C		intron	N/A	ENSP00000507293.1
	UBAP2	ENST00000684158.1		c.521-89T>C		intron	N/A	ENSP00000508372.1

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

African (AFR) AF: 0.231 AC: 6552 AN: 28354

American (AMR) AF: 0.144 AC: 5978 AN: 41618

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 3631 AN: 24050

East Asian (EAS) AF: 0.222 AC: 8480 AN: 38278

South Asian (SAS) AF: 0.347 AC: 27425 AN: 79080

European-Finnish (FIN) AF: 0.195 AC: 10252 AN: 52586

Middle Eastern (MID) AF: 0.162 AC: 851 AN: 5248

European-Non Finnish (NFE) AF: 0.165 AC: 148570 AN: 898240

Other (OTH) AF: 0.183 AC: 9540 AN: 51992

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

African (AFR) AF: 0.232 AC: 9615 AN: 41490

American (AMR) AF: 0.165 AC: 2516 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 511 AN: 3470

East Asian (EAS) AF: 0.178 AC: 922 AN: 5176

South Asian (SAS) AF: 0.358 AC: 1726 AN: 4822

European-Finnish (FIN) AF: 0.185 AC: 1959 AN: 10588

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.169 AC: 11472 AN: 67968

Other (OTH) AF: 0.185 AC: 390 AN: 2108

Alfa AF: 0.183 Hom.: 1479

Bravo AF: 0.185

Asia WGS AF: 0.269 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.3
DANN	Benign	0.76
PhyloP100		1.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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