dbSNP rs1332944: OBI1-AS1:n.230+169471A>C (chr13-78089389-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000607862.5(OBI1-AS1):n.230+169471A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 151,982 control chromosomes in the GnomAD database, including 37,130 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 0.69 ( 37130 hom., cov: 31)

Consequence

OBI1-AS1
ENST00000607862.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0530

Publications

0 publications found

Variant links:

Genes affected

OBI1-AS1 (HGNC:42700): (OBI1 antisense RNA 1)

OBI1-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=-0.77).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OBI1-AS1	NR_047001.1 link	n.210+34325A>C		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
OBI1-AS1	ENST00000607862.5 link	n.230+169471A>C	intron_variant	Intron 1 of 2	1
OBI1-AS1	ENST00000430549.6 link	n.68+34325A>C	intron_variant	Intron 1 of 4	4
OBI1-AS1	ENST00000444769.7 link	n.42+34325A>C	intron_variant	Intron 1 of 5	4

Frequencies

GnomAD3 genomes

AF:

0.686

AC:

104212

AN:

151864

Hom.:

37123

Cov.:

show subpopulations

Gnomad AFR

AF:

0.485

Gnomad AMI

AF:

0.684

Gnomad AMR

AF:

0.775

Gnomad ASJ

AF:

0.635

Gnomad EAS

AF:

0.964

Gnomad SAS

AF:

0.781

Gnomad FIN

AF:

0.789

Gnomad MID

AF:

0.726

Gnomad NFE

AF:

0.747

Gnomad OTH

AF:

0.689

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

GnomAD4 genome

AF:

0.686

AC:

104245

AN:

151982

Hom.:

37130

Cov.:

AF XY:

0.692

AC XY:

51413

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.485

AC:

20080

AN:

41434

American (AMR)

AF:

0.776

AC:

11831

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.635

AC:

2196

AN:

3460

East Asian (EAS)

AF:

0.964

AC:

4995

AN:

5180

South Asian (SAS)

AF:

0.782

AC:

3765

AN:

4814

European-Finnish (FIN)

AF:

0.789

AC:

8331

AN:

10554

Middle Eastern (MID)

AF:

0.719

AC:

210

AN:

292

European-Non Finnish (NFE)

AF:

0.747

AC:

50761

AN:

67972

Other (OTH)

AF:

0.688

AC:

1452

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1576

3153

4729

6306

7882

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

812

1624

2436

3248

4060

<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:

0.721

Hom.:

5036

Bravo

AF:

0.675

Asia WGS

AF:

0.838

AC:

2912

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

1.4

(source)

DANN

Benign

0.91

PhyloP100

0.053

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