Genetic Variant NM_001144072.2:c.807+11289G>A (chr13-99351854-G-A) – 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.807+11289G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 440,372 control chromosomes in the GnomAD database, including 5,468 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 0.13 ( 1578 hom., cov: 32)

Exomes 𝑓: 0.15 ( 3890 hom. )

Consequence

UBAC2
NM_001144072.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.258

Publications

20 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:

FKSG29 (HGNC:):

FKSG29 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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
UBAC2	NM_001144072.2	MANE Select	c.807+11289G>A	intron	N/A	NP_001137544.1	Q8NBM4-1
UBAC2	NM_177967.4		c.702+11289G>A	intron	N/A	NP_808882.1	Q8NBM4-2
FKSG29	NR_024013.1		n.435G>A	non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
UBAC2	ENST00000403766.8	TSL:2 MANE Select	c.807+11289G>A	intron	N/A	ENSP00000383911.3	Q8NBM4-1
UBAC2	ENST00000473194.5	TSL:1	n.574+11289G>A	intron	N/A
UBAC2	ENST00000480738.1	TSL:1	n.426+11289G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.133

AC:

20190

AN:

152084

Hom.:

1570

Cov.:

show subpopulations

Gnomad AFR

AF:

0.113

Gnomad AMI

AF:

0.0373

Gnomad AMR

AF:

0.208

Gnomad ASJ

AF:

0.0890

Gnomad EAS

AF:

0.322

Gnomad SAS

AF:

0.165

Gnomad FIN

AF:

0.134

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.138

GnomAD2 exomes

AF:

0.172

AC:

21828

AN:

126770

AF XY:

0.166

show subpopulations

Gnomad AFR exome

AF:

0.107

Gnomad AMR exome

AF:

0.313

Gnomad ASJ exome

AF:

0.0879

Gnomad EAS exome

AF:

0.317

Gnomad FIN exome

AF:

0.131

Gnomad NFE exome

AF:

0.110

Gnomad OTH exome

AF:

0.137

GnomAD4 exome

AF:

0.146

AC:

42077

AN:

288170

Hom.:

3890

Cov.:

AF XY:

0.146

AC XY:

23783

AN XY:

162988

show subpopulations

African (AFR)

AF:

0.106

AC:

850

AN:

8046

American (AMR)

AF:

0.310

AC:

7819

AN:

25206

Ashkenazi Jewish (ASJ)

AF:

0.0858

AC:

866

AN:

10098

East Asian (EAS)

AF:

0.320

AC:

2850

AN:

8906

South Asian (SAS)

AF:

0.167

AC:

9662

AN:

57858

European-Finnish (FIN)

AF:

0.134

AC:

1675

AN:

12478

Middle Eastern (MID)

AF:

0.0885

AC:

240

AN:

2712

European-Non Finnish (NFE)

AF:

0.110

AC:

16436

AN:

149440

Other (OTH)

AF:

0.125

AC:

1679

AN:

13426

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

1707

3413

5120

6826

8533

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

226

452

678

904

1130

<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:

0.133

AC:

20212

AN:

152202

Hom.:

1578

Cov.:

AF XY:

0.136

AC XY:

10109

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.113

AC:

4700

AN:

41530

American (AMR)

AF:

0.209

AC:

3194

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0890

AC:

309

AN:

3470

East Asian (EAS)

AF:

0.322

AC:

1664

AN:

5168

South Asian (SAS)

AF:

0.164

AC:

790

AN:

4826

European-Finnish (FIN)

AF:

0.134

AC:

1421

AN:

10592

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.115

AC:

7792

AN:

68018

Other (OTH)

AF:

0.140

AC:

294

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

867

1733

2600

3466

4333

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

230

460

690

920

1150

<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:

0.122

Hom.:

2525

Bravo

AF:

0.140

Asia WGS

AF:

0.248

AC:

860

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

(source)

DANN

Benign

0.54

PhyloP100

0.26

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over