chr13-99331065-G-A

Variant names:

• chr13-99331065-G-A
• rs2181502
• NM_001144072.2:c.562-9255G>A

Variant summary

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

The NM_001144072.2(UBAC2):​c.562-9255G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 151,966 control chromosomes in the GnomAD database, including 27,024 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 (27024 hom., cov: 31)
• Consequence: UBAC2 NM_001144072.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 6 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.707 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBAC2	NM_001144072.2	MANE Select	c.562-9255G>A		intron	N/A	NP_001137544.1
	UBAC2	NM_177967.4		c.457-9255G>A		intron	N/A	NP_808882.1
	UBAC2	NR_026644.2		n.1245-9255G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBAC2	ENST00000403766.8	TSL:2 MANE Select	c.562-9255G>A		intron	N/A	ENSP00000383911.3
	UBAC2	ENST00000473194.5	TSL:1	n.329-9255G>A		intron	N/A
	UBAC2	ENST00000480738.1	TSL:1	n.181-9255G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87666 AN: 151848 Hom.: 27014 Cov.: 31

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.577 AC: 87718 AN: 151966 Hom.: 27024 Cov.: 31 AF XY: 0.570 AC XY: 42348 AN XY: 74288

African (AFR) AF: 0.366 AC: 15149 AN: 41406

American (AMR) AF: 0.549 AC: 8383 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2214 AN: 3470

East Asian (EAS) AF: 0.494 AC: 2552 AN: 5170

South Asian (SAS) AF: 0.455 AC: 2193 AN: 4816

European-Finnish (FIN) AF: 0.628 AC: 6620 AN: 10544

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48425 AN: 67968

Other (OTH) AF: 0.577 AC: 1217 AN: 2110

Alfa AF: 0.671 Hom.: 58592

Bravo AF: 0.565

Asia WGS AF: 0.415 AC: 1446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.66
PhyloP100		-0.046
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: rs2181502; hg19: chr13-99983319;