dbSNP rs9544725: OBI1-AS1:n.231-119021A>G (chr13-78155232-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 ENST00000607862.5(OBI1-AS1):n.231-119021A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 152,036 control chromosomes in the GnomAD database, including 34,097 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 0.66 ( 34097 hom., cov: 32)

Consequence

OBI1-AS1
ENST00000607862.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.520

Publications

4 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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OBI1-AS1	NR_047001.1 link	n.211-34376A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
OBI1-AS1	ENST00000607862.5 link	n.231-119021A>G	intron_variant	Intron 1 of 2	1
OBI1-AS1	ENST00000430549.6 link	n.69-34376A>G	intron_variant	Intron 1 of 4	4
OBI1-AS1	ENST00000444769.7 link	n.43-34376A>G	intron_variant	Intron 1 of 5	4

Frequencies

GnomAD3 genomes

AF:

0.662

AC:

100571

AN:

151918

Hom.:

34079

Cov.:

show subpopulations

Gnomad AFR

AF:

0.520

Gnomad AMI

AF:

0.598

Gnomad AMR

AF:

0.746

Gnomad ASJ

AF:

0.636

Gnomad EAS

AF:

0.812

Gnomad SAS

AF:

0.631

Gnomad FIN

AF:

0.725

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.713

Gnomad OTH

AF:

0.664

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

GnomAD4 genome

AF:

0.662

AC:

100622

AN:

152036

Hom.:

34097

Cov.:

AF XY:

0.662

AC XY:

49205

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.520

AC:

21536

AN:

41448

American (AMR)

AF:

0.747

AC:

11401

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.636

AC:

2206

AN:

3470

East Asian (EAS)

AF:

0.813

AC:

4198

AN:

5164

South Asian (SAS)

AF:

0.632

AC:

3044

AN:

4820

European-Finnish (FIN)

AF:

0.725

AC:

7655

AN:

10564

Middle Eastern (MID)

AF:

0.548

AC:

161

AN:

294

European-Non Finnish (NFE)

AF:

0.713

AC:

48476

AN:

67988

Other (OTH)

AF:

0.663

AC:

1400

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1695

3390

5085

6780

8475

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

798

1596

2394

3192

3990

<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:

0.694

Hom.:

119274

Bravo

AF:

0.661

Asia WGS

AF:

0.681

AC:

2370

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.6

(source)

DANN

Benign

0.67

PhyloP100

0.52

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