Genetic Variant UBAC2:c.32-3919A>G (chr13-99234508-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001144072.2(UBAC2):c.32-3919A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 156,892 control chromosomes in the GnomAD database, including 26,410 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 0.55 ( 25491 hom., cov: 32)

Exomes 𝑓: 0.61 ( 919 hom. )

Consequence

UBAC2
NM_001144072.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.04

Publications

7 publications found

Variant links:

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 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBAC2	NM_001144072.2 link	c.32-3919A>G		intron_variant	Intron 1 of 8	ENST00000403766.8	NP_001137544.1	Q8NBM4-1A0A024RE02A8K2S7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBAC2	ENST00000403766.8 link	c.32-3919A>G		intron_variant	Intron 1 of 8	2	NM_001144072.2	ENSP00000383911.3		Q8NBM4-1

Frequencies

GnomAD3 genomes

AF:

0.549

AC:

83395

AN:

151944

Hom.:

25487

Cov.:

show subpopulations

Gnomad AFR

AF:

0.275

Gnomad AMI

AF:

0.846

Gnomad AMR

AF:

0.535

Gnomad ASJ

AF:

0.638

Gnomad EAS

AF:

0.490

Gnomad SAS

AF:

0.449

Gnomad FIN

AF:

0.626

Gnomad MID

AF:

0.637

Gnomad NFE

AF:

0.709

Gnomad OTH

AF:

0.563

GnomAD4 exome

AF:

0.608

AC:

2936

AN:

4830

Hom.:

919

AF XY:

0.583

AC XY:

1790

AN XY:

3072

show subpopulations

African (AFR)

AF:

0.350

AC:

AN:

American (AMR)

AF:

0.525

AC:

AN:

162

Ashkenazi Jewish (ASJ)

AF:

0.783

AC:

AN:

East Asian (EAS)

AF:

0.278

AC:

AN:

South Asian (SAS)

AF:

0.467

AC:

769

AN:

1648

European-Finnish (FIN)

AF:

0.640

AC:

142

AN:

222

Middle Eastern (MID)

AF:

0.583

AC:

AN:

European-Non Finnish (NFE)

AF:

0.704

AC:

1772

AN:

2516

Other (OTH)

AF:

0.625

AC:

AN:

152

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

111

166

222

277

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.549

AC:

83420

AN:

152062

Hom.:

25491

Cov.:

AF XY:

0.543

AC XY:

40336

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.275

AC:

11410

AN:

41484

American (AMR)

AF:

0.535

AC:

8176

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.638

AC:

2211

AN:

3464

East Asian (EAS)

AF:

0.491

AC:

2532

AN:

5162

South Asian (SAS)

AF:

0.450

AC:

2170

AN:

4820

European-Finnish (FIN)

AF:

0.626

AC:

6623

AN:

10572

Middle Eastern (MID)

AF:

0.654

AC:

191

AN:

292

European-Non Finnish (NFE)

AF:

0.709

AC:

48162

AN:

67964

Other (OTH)

AF:

0.559

AC:

1173

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1713

3426

5140

6853

8566

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

704

1408

2112

2816

3520

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.562

Hom.:

5734

Bravo

AF:

0.533

Asia WGS

AF:

0.405

AC:

1411

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.55

(source)

DANN

Benign

0.56

PhyloP100

-1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over