rs2182885

chr13-99202870-G-A

Variant summary

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

The NM_001144072.2(UBAC2):c.31+1931G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151,958 control chromosomes in the GnomAD database, including 18,426 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 0.46 (18426 hom., cov: 31)
• Consequence: UBAC2 NM_001144072.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBAC2	NM_001144072.2	c.31+1931G>A		intron_variant		ENST00000403766.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBAC2	ENST00000403766.8	c.31+1931G>A		intron_variant		2	NM_001144072.2	P1

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69724 AN: 151840 Hom.: 18419 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.459 AC: 69755 AN: 151958 Hom.: 18426 Cov.: 31 AF XY: 0.454 AC XY: 33695 AN XY: 74286

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.477

Alfa AF: 0.514 Hom.: 3676

Bravo AF: 0.447

Asia WGS AF: 0.297 AC: 1034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.16
Dann	Benign	0.62

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: rs2182885; hg19: chr13-99855124;