chr13-99380148-G-T

Variant names:

• chr13-99380148-G-T
• rs912130
• NM_001144072.2:c.928-5080G>T

Variant summary

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

The NM_001144072.2(UBAC2):​c.928-5080G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 152,094 control chromosomes in the GnomAD database, including 26,916 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 0.58 (26916 hom., cov: 33)
• Consequence: UBAC2 NM_001144072.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001144072.2. 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
	UBAC2	NM_001144072.2	MANE Select	c.928-5080G>T		intron	N/A	NP_001137544.1
	UBAC2	NM_177967.4		c.823-5080G>T		intron	N/A	NP_808882.1
	UBAC2	NR_026644.2		n.1611-5080G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBAC2	ENST00000403766.8	TSL:2 MANE Select	c.928-5080G>T		intron	N/A	ENSP00000383911.3
	UBAC2	ENST00000473194.5	TSL:1	n.695-5080G>T		intron	N/A
	UBAC2	ENST00000480738.1	TSL:1	n.547-5080G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87550 AN: 151976 Hom.: 26909 Cov.: 33

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.576 AC: 87590 AN: 152094 Hom.: 26916 Cov.: 33 AF XY: 0.569 AC XY: 42318 AN XY: 74356

African (AFR) AF: 0.365 AC: 15129 AN: 41470

American (AMR) AF: 0.545 AC: 8327 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2204 AN: 3468

East Asian (EAS) AF: 0.501 AC: 2597 AN: 5184

South Asian (SAS) AF: 0.462 AC: 2229 AN: 4824

European-Finnish (FIN) AF: 0.626 AC: 6612 AN: 10566

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48308 AN: 67980

Other (OTH) AF: 0.576 AC: 1217 AN: 2112

Alfa AF: 0.611 Hom.: 5231

Bravo AF: 0.564

Asia WGS AF: 0.424 AC: 1478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.28
DANN	Benign	0.67
PhyloP100		-1.3
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: rs912130; hg19: chr13-100032402;