13-99315897-A-G

Variant names:

• chr13-99315897-A-G
• rs9517683
• NM_001144072.2:c.513+1677A>G

Variant summary

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

The NM_001144072.2(UBAC2):​c.513+1677A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 151,596 control chromosomes in the GnomAD database, including 9,368 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 0.33 (9368 hom., cov: 29)
• Consequence: UBAC2 NM_001144072.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.696

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBAC2	NM_001144072.2	c.513+1677A>G		intron_variant	Intron 5 of 8	ENST00000403766.8	NP_001137544.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBAC2	ENST00000403766.8	c.513+1677A>G		intron_variant	Intron 5 of 8	2	NM_001144072.2	ENSP00000383911.3

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50458 AN: 151478 Hom.: 9356 Cov.: 29

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.333 AC: 50513 AN: 151596 Hom.: 9368 Cov.: 29 AF XY: 0.343 AC XY: 25416 AN XY: 74038

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.596

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.313

Alfa AF: 0.244 Hom.: 2674

Bravo AF: 0.337

Asia WGS AF: 0.555 AC: 1927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.45

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: rs9517683; hg19: chr13-99968151;