chr13-99381862-A-G

Position:

• chr13-99381862-A-G

Variant summary

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

The NM_001144072.2(UBAC2):​c.928-3366A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 152,156 control chromosomes in the GnomAD database, including 52,002 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 0.82 (52002 hom., cov: 32)
• Consequence: UBAC2 NM_001144072.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBAC2	NM_001144072.2	c.928-3366A>G		intron_variant		ENST00000403766.8	NP_001137544.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBAC2	ENST00000403766.8	c.928-3366A>G		intron_variant		2	NM_001144072.2	ENSP00000383911	P1

Frequencies

GnomAD3 genomes AF: 0.823 AC: 125129 AN: 152038 Hom.: 51974 Cov.: 32

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.829

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

GnomAD4 genome AF: 0.823 AC: 125201 AN: 152156 Hom.: 52002 Cov.: 32 AF XY: 0.822 AC XY: 61124 AN XY: 74366

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.777

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.885

Gnomad4 OTH AF: 0.827

Alfa AF: 0.836 Hom.: 9049

Bravo AF: 0.811

Asia WGS AF: 0.736 AC: 2562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.15
DANN	Benign	0.60

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: rs4772190; hg19: chr13-100034116;