chr13-99220179-G-C

Variant names:

• chr13-99220179-G-C
• rs984477
• NM_001144072.2:c.32-18248G>C

Variant summary

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

The NM_001144072.2(UBAC2):​c.32-18248G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 152,006 control chromosomes in the GnomAD database, including 22,947 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 0.53 (22947 hom., cov: 32)
• Consequence: UBAC2 NM_001144072.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880
• Publications: 5 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.643 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.32-18248G>C		intron	N/A	NP_001137544.1
	UBAC2	NM_177967.4		c.157-18248G>C		intron	N/A	NP_808882.1
	UBAC2	NR_026644.2		n.715-18248G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBAC2	ENST00000403766.8	TSL:2 MANE Select	c.32-18248G>C		intron	N/A	ENSP00000383911.3
	UBAC2	ENST00000376440.6	TSL:2	c.157-18248G>C		intron	N/A	ENSP00000365623.2
	UBAC2	ENST00000355700.9	TSL:3	c.32-18248G>C		intron	N/A	ENSP00000347928.5

Frequencies

GnomAD3 genomes AF: 0.533 AC: 81006 AN: 151888 Hom.: 22935 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.533 AC: 81052 AN: 152006 Hom.: 22947 Cov.: 32 AF XY: 0.526 AC XY: 39084 AN XY: 74298

African (AFR) AF: 0.348 AC: 14434 AN: 41458

American (AMR) AF: 0.520 AC: 7926 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2137 AN: 3470

East Asian (EAS) AF: 0.501 AC: 2592 AN: 5170

South Asian (SAS) AF: 0.453 AC: 2189 AN: 4828

European-Finnish (FIN) AF: 0.533 AC: 5605 AN: 10522

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

European-Non Finnish (NFE) AF: 0.648 AC: 44055 AN: 67994

Other (OTH) AF: 0.540 AC: 1136 AN: 2102

Alfa AF: 0.578 Hom.: 3154

Bravo AF: 0.528

Asia WGS AF: 0.415 AC: 1438 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.72
DANN	Benign	0.42
PhyloP100		0.088
Mutation Taster		=99/1	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: rs984477; hg19: chr13-99872433;