13-99369264-T-G

Position:

• chr13-99369264-T-G

Variant summary

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

The NM_001144072.2(UBAC2):​c.927+1358T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.839 in 152,164 control chromosomes in the GnomAD database, including 53,804 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 0.84 (53804 hom., cov: 31)
• Consequence: UBAC2 NM_001144072.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

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]

UBAC2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• 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.927+1358T>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.927+1358T>G		intron_variant		2	NM_001144072.2	ENSP00000383911.3

Frequencies

GnomAD3 genomes AF: 0.839 AC: 127526 AN: 152046 Hom.: 53769 Cov.: 31

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.839 AC: 127607 AN: 152164 Hom.: 53804 Cov.: 31 AF XY: 0.837 AC XY: 62252 AN XY: 74394

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.782

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.681

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.885

Gnomad4 OTH AF: 0.839

Alfa AF: 0.833 Hom.: 9284

Bravo AF: 0.829

Asia WGS AF: 0.746 AC: 2599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.41

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: rs4636771; hg19: chr13-100021518;