Genetic Variant UBAC2-AS1:n.375+2903A>G (chr13-99194645-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000662755.1(UBAC2-AS1):n.375+2903A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 151,998 control chromosomes in the GnomAD database, including 27,028 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 0.58 ( 27028 hom., cov: 31)

Consequence

UBAC2-AS1
ENST00000662755.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.95

Publications

6 publications found

Variant links:

Genes affected

UBAC2-AS1 (HGNC:42502): (UBAC2 antisense RNA 1)

UBAC2-AS1 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=-1.0).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
UBAC2-AS1	ENST00000662755.1 link	n.375+2903A>G	intron_variant	Intron 2 of 2
UBAC2-AS1	ENST00000668596.2 link	n.386+2903A>G	intron_variant	Intron 2 of 3
UBAC2-AS1	ENST00000671580.2 link	n.653+2903A>G	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.578

AC:

87729

AN:

151880

Hom.:

27019

Cov.:

show subpopulations

Gnomad AFR

AF:

0.366

Gnomad AMI

AF:

0.875

Gnomad AMR

AF:

0.547

Gnomad ASJ

AF:

0.638

Gnomad EAS

AF:

0.502

Gnomad SAS

AF:

0.459

Gnomad FIN

AF:

0.628

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.712

Gnomad OTH

AF:

0.578

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

GnomAD4 genome

AF:

0.577

AC:

87776

AN:

151998

Hom.:

27028

Cov.:

AF XY:

0.570

AC XY:

42391

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.366

AC:

15171

AN:

41414

American (AMR)

AF:

0.546

AC:

8343

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.638

AC:

2213

AN:

3470

East Asian (EAS)

AF:

0.503

AC:

2605

AN:

5178

South Asian (SAS)

AF:

0.461

AC:

2219

AN:

4818

European-Finnish (FIN)

AF:

0.628

AC:

6626

AN:

10548

Middle Eastern (MID)

AF:

0.667

AC:

196

AN:

294

European-Non Finnish (NFE)

AF:

0.712

AC:

48391

AN:

67984

Other (OTH)

AF:

0.576

AC:

1214

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1728

3457

5185

6914

8642

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

732

1464

2196

2928

3660

<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:

0.613

Hom.:

5235

Bravo

AF:

0.566

Asia WGS

AF:

0.423

AC:

1475

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.37

(source)

DANN

Benign

0.31

PhyloP100

-3.0

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over