Genetic Variant UBAC2:c.*644A>G (chr13-99385979-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.*644A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 152,588 control chromosomes in the GnomAD database, including 30,415 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 0.63 ( 30287 hom., cov: 33)

Exomes 𝑓: 0.71 ( 128 hom. )

Consequence

UBAC2
NM_001144072.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.115

Publications

27 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:

Genome browser will be placed here

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=-0.62).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.648 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
UBAC2	NM_001144072.2	MANE Select	c.*644A>G	3_prime_UTR	Exon 9 of 9	NP_001137544.1
UBAC2	NR_026644.2		n.2362A>G	non_coding_transcript_exon	Exon 9 of 9
UBAC2	NM_177967.4		c.*644A>G	3_prime_UTR	Exon 7 of 7	NP_808882.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
UBAC2	ENST00000403766.8	TSL:2 MANE Select	c.*644A>G	3_prime_UTR	Exon 9 of 9	ENSP00000383911.3
UBAC2	ENST00000460562.5	TSL:2	n.1895A>G	non_coding_transcript_exon	Exon 6 of 6
UBAC2	ENST00000494576.5	TSL:2	n.1400A>G	non_coding_transcript_exon	Exon 6 of 6

Frequencies

GnomAD3 genomes

AF:

0.629

AC:

95526

AN:

151960

Hom.:

30269

Cov.:

show subpopulations

Gnomad AFR

AF:

0.571

Gnomad AMI

AF:

0.601

Gnomad AMR

AF:

0.594

Gnomad ASJ

AF:

0.631

Gnomad EAS

AF:

0.615

Gnomad SAS

AF:

0.642

Gnomad FIN

AF:

0.752

Gnomad MID

AF:

0.684

Gnomad NFE

AF:

0.653

Gnomad OTH

AF:

0.604

GnomAD4 exome

AF:

0.714

AC:

364

AN:

510

Hom.:

128

Cov.:

AF XY:

0.712

AC XY:

225

AN XY:

316

show subpopulations

African (AFR)

AF:

0.750

AC:

AN:

American (AMR)

AF:

0.857

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

0.750

AC:

AN:

South Asian (SAS)

AF:

0.800

AC:

AN:

European-Finnish (FIN)

AF:

0.730

AC:

200

AN:

274

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.670

AC:

130

AN:

194

Other (OTH)

AF:

0.750

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

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:

0.629

AC:

95582

AN:

152078

Hom.:

30287

Cov.:

AF XY:

0.632

AC XY:

47001

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.571

AC:

23667

AN:

41444

American (AMR)

AF:

0.594

AC:

9085

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.631

AC:

2190

AN:

3470

East Asian (EAS)

AF:

0.614

AC:

3178

AN:

5172

South Asian (SAS)

AF:

0.643

AC:

3100

AN:

4820

European-Finnish (FIN)

AF:

0.752

AC:

7954

AN:

10578

Middle Eastern (MID)

AF:

0.677

AC:

199

AN:

294

European-Non Finnish (NFE)

AF:

0.653

AC:

44391

AN:

67990

Other (OTH)

AF:

0.603

AC:

1271

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1812

3625

5437

7250

9062

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

788

1576

2364

3152

3940

<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:

0.636

Hom.:

104685

Bravo

AF:

0.612

Asia WGS

AF:

0.613

AC:

2137

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

7.0

(source)

DANN

Benign

0.84

PhyloP100

-0.12

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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