dbSNP rs11069357: UBAC2-AS1:n.500T>C (chr13-99197376-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 ENST00000445737.2(UBAC2-AS1):n.500T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 152,034 control chromosomes in the GnomAD database, including 27,042 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 ( 27017 hom., cov: 30)

Exomes 𝑓: 0.73 ( 25 hom. )

Consequence

UBAC2-AS1
ENST00000445737.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0510

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=-0.96).

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
UBAC2-AS1	NR_036531.1 link	n.819T>C		non_coding_transcript_exon_variant	Exon 2 of 2
UBAC2-AS1	NR_036532.1 link	n.545T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
UBAC2-AS1	ENST00000445737.2 link	n.500T>C	non_coding_transcript_exon_variant	Exon 2 of 2	1
UBAC2-AS1	ENST00000426037.9 link	n.832T>C	non_coding_transcript_exon_variant	Exon 2 of 2	2
UBAC2-AS1	ENST00000658188.1 link	n.763T>C	non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.577

AC:

87674

AN:

151830

Hom.:

27006

Cov.:

show subpopulations

Gnomad AFR

AF:

0.366

Gnomad AMI

AF:

0.875

Gnomad AMR

AF:

0.546

Gnomad ASJ

AF:

0.638

Gnomad EAS

AF:

0.500

Gnomad SAS

AF:

0.459

Gnomad FIN

AF:

0.629

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.712

Gnomad OTH

AF:

0.578

GnomAD4 exome

AF:

0.733

AC:

AN:

Hom.:

Cov.:

AF XY:

0.726

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.730

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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:

0.577

AC:

87724

AN:

151948

Hom.:

27017

Cov.:

AF XY:

0.570

AC XY:

42360

AN XY:

74268

show subpopulations

African (AFR)

AF:

0.366

AC:

15157

AN:

41414

American (AMR)

AF:

0.546

AC:

8334

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.638

AC:

2214

AN:

3470

East Asian (EAS)

AF:

0.501

AC:

2581

AN:

5150

South Asian (SAS)

AF:

0.460

AC:

2217

AN:

4816

European-Finnish (FIN)

AF:

0.629

AC:

6636

AN:

10544

Middle Eastern (MID)

AF:

0.667

AC:

196

AN:

294

European-Non Finnish (NFE)

AF:

0.712

AC:

48375

AN:

67964

Other (OTH)

AF:

0.577

AC:

1218

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1720

3440

5159

6879

8599

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

730

1460

2190

2920

3650

<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:

0.628

Hom.:

4074

Bravo

AF:

0.566

Asia WGS

AF:

0.425

AC:

1480

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

4.0

(source)

DANN

Benign

0.44

PhyloP100

0.051

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over