rs9517668

Variant names:

• chr13-99271586-T-A
• rs9517668
• NM_001144072.2:c.389+26962T>A

Your query was ambiguous. Multiple possible variants found:

• chr13-99271586-T-A
• chr13-99271586-T-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001144072.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBAC2	NM_001144072.2	MANE Select	c.389+26962T>A		intron	N/A	NP_001137544.1	Q8NBM4-1
	UBAC2	NM_177967.4		c.284+33032T>A		intron	N/A	NP_808882.1	Q8NBM4-2
	UBAC2	NR_026644.2		n.1072+26962T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBAC2	ENST00000403766.8	TSL:2 MANE Select	c.389+26962T>A		intron	N/A	ENSP00000383911.3	Q8NBM4-1
	UBAC2	ENST00000961156.1		c.389+26962T>A		intron	N/A	ENSP00000631215.1
	UBAC2	ENST00000858721.1		c.437+16632T>A		intron	N/A	ENSP00000528780.1

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

African (AFR) AF: 0.651 AC: 26992 AN: 41476

American (AMR) AF: 0.769 AC: 11758 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3160 AN: 3472

East Asian (EAS) AF: 0.678 AC: 3511 AN: 5178

South Asian (SAS) AF: 0.831 AC: 4015 AN: 4832

European-Finnish (FIN) AF: 0.868 AC: 9212 AN: 10616

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.884 AC: 60142 AN: 68006

Other (OTH) AF: 0.815 AC: 1721 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0010
DANN	Benign	0.49
PhyloP100		-3.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9517668; hg19: chr13-99923840;