NM_001144072.2:c.927+3309G>A

Variant names:

• chr13-99371215-G-A
• rs7332161
• NM_001144072.2:c.927+3309G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001144072.2(UBAC2):​c.927+3309G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,024 control chromosomes in the GnomAD database, including 1,574 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 0.13 (1574 hom., cov: 32)
• Consequence: UBAC2 NM_001144072.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60
• Publications: 9 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBAC2	NM_001144072.2	c.927+3309G>A		intron_variant	Intron 8 of 8	ENST00000403766.8	NP_001137544.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBAC2	ENST00000403766.8	c.927+3309G>A		intron_variant	Intron 8 of 8	2	NM_001144072.2	ENSP00000383911.3

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20181 AN: 151908 Hom.: 1566 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.0894

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.133 AC: 20202 AN: 152024 Hom.: 1574 Cov.: 32 AF XY: 0.136 AC XY: 10109 AN XY: 74310

African (AFR) AF: 0.113 AC: 4704 AN: 41468

American (AMR) AF: 0.209 AC: 3199 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0894 AC: 310 AN: 3468

East Asian (EAS) AF: 0.321 AC: 1657 AN: 5170

South Asian (SAS) AF: 0.168 AC: 808 AN: 4816

European-Finnish (FIN) AF: 0.134 AC: 1416 AN: 10544

Middle Eastern (MID) AF: 0.0479 AC: 14 AN: 292

European-Non Finnish (NFE) AF: 0.114 AC: 7760 AN: 67958

Other (OTH) AF: 0.142 AC: 300 AN: 2110

Alfa AF: 0.138 Hom.: 310

Bravo AF: 0.140

Asia WGS AF: 0.249 AC: 862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	18
DANN	Benign	0.65
PhyloP100		1.6
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: rs7332161; hg19: chr13-100023469;