rs9517668

chr13-99271586-T-Achr13-99271586-T-C

Variant summary

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

The NM_001144072.2(UBAC2):c.389+26962T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.799 in 152,192 control chromosomes in the GnomAD database, including 49,504 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 0.80 (49504 hom., cov: 32)
• Consequence: UBAC2 NM_001144072.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBAC2	NM_001144072.2	c.389+26962T>A		intron_variant		ENST00000403766.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBAC2	ENST00000403766.8	c.389+26962T>A		intron_variant		2	NM_001144072.2	P1

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121584 AN: 152074 Hom.: 49476 Cov.: 32

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.799 AC: 121657 AN: 152192 Hom.: 49504 Cov.: 32 AF XY: 0.799 AC XY: 59482 AN XY: 74424

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.769

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.831

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.884

Gnomad4 OTH AF: 0.815

Alfa AF: 0.836 Hom.: 6663

Bravo AF: 0.784

Asia WGS AF: 0.729 AC: 2539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.0010
Dann	Benign	0.49

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: rs9517668; hg19: chr13-99923840;