rs9554573

chr13-99234508-A-G

Variant summary

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

The NM_001144072.2(UBAC2):c.32-3919A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 156,892 control chromosomes in the GnomAD database, including 26,410 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 0.55 (25491 hom., cov: 32)
  • Exomes 𝑓: 0.61 (919 hom.)
• Consequence: UBAC2 NM_001144072.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

UBAC2 (HGNC:20486): (UBA domain containing 2) Involved in negative regulation of canonical Wnt signaling pathway and negative regulation of retrograde protein transport, ER to cytosol. Acts upstream of or within protein localization to endoplasmic reticulum. Located in endoplasmic reticulum. [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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBAC2	NM_001144072.2	c.32-3919A>G		intron_variant		ENST00000403766.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBAC2	ENST00000403766.8	c.32-3919A>G		intron_variant		2	NM_001144072.2	P1

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83395 AN: 151944 Hom.: 25487 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.563

GnomAD4 exome AF: 0.608 AC: 2936 AN: 4830 Hom.: 919 AF XY: 0.583 AC XY: 1790 AN XY: 3072

Gnomad4 AFR exome AF: 0.350

Gnomad4 AMR exome AF: 0.525

Gnomad4 ASJ exome AF: 0.783

Gnomad4 EAS exome AF: 0.278

Gnomad4 SAS exome AF: 0.467

Gnomad4 FIN exome AF: 0.640

Gnomad4 NFE exome AF: 0.704

Gnomad4 OTH exome AF: 0.625

GnomAD4 genome AF: 0.549 AC: 83420 AN: 152062 Hom.: 25491 Cov.: 32 AF XY: 0.543 AC XY: 40336 AN XY: 74352

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.559

Alfa AF: 0.569 Hom.: 5703

Bravo AF: 0.533

Asia WGS AF: 0.405 AC: 1411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.55
Dann	Benign	0.56

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: rs9554573; hg19: chr13-99886762;