Genetic Variant OBI1-AS1:n.315+56771G>T (chr13-78331108-G-T) – 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.315+56771G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 152,016 control chromosomes in the GnomAD database, including 31,825 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 0.64 ( 31825 hom., cov: 33)

Consequence

OBI1-AS1
ENST00000607862.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0760

Publications

1 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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OBI1-AS1	NR_047001.1 link	n.384+56771G>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
OBI1-AS1	ENST00000607862.5 link	n.315+56771G>T	intron_variant	Intron 2 of 2	1
OBI1-AS1	ENST00000430549.6 link	n.242+56771G>T	intron_variant	Intron 3 of 4	4
OBI1-AS1	ENST00000444769.7 link	n.216+56771G>T	intron_variant	Intron 3 of 5	4

Frequencies

GnomAD3 genomes

AF:

0.643

AC:

97731

AN:

151898

Hom.:

31783

Cov.:

show subpopulations

Gnomad AFR

AF:

0.708

Gnomad AMI

AF:

0.535

Gnomad AMR

AF:

0.675

Gnomad ASJ

AF:

0.600

Gnomad EAS

AF:

0.683

Gnomad SAS

AF:

0.489

Gnomad FIN

AF:

0.713

Gnomad MID

AF:

0.472

Gnomad NFE

AF:

0.599

Gnomad OTH

AF:

0.635

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

GnomAD4 genome

AF:

0.644

AC:

97824

AN:

152016

Hom.:

31825

Cov.:

AF XY:

0.645

AC XY:

47936

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.709

AC:

29410

AN:

41494

American (AMR)

AF:

0.675

AC:

10296

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.600

AC:

2079

AN:

3464

East Asian (EAS)

AF:

0.684

AC:

3530

AN:

5162

South Asian (SAS)

AF:

0.488

AC:

2351

AN:

4818

European-Finnish (FIN)

AF:

0.713

AC:

7556

AN:

10598

Middle Eastern (MID)

AF:

0.456

AC:

134

AN:

294

European-Non Finnish (NFE)

AF:

0.599

AC:

40654

AN:

67912

Other (OTH)

AF:

0.630

AC:

1326

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1766

3533

5299

7066

8832

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

782

1564

2346

3128

3910

<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:

0.588

Hom.:

12111

Bravo

AF:

0.647

Asia WGS

AF:

0.590

AC:

2048

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.99

(source)

DANN

Benign

0.22

PhyloP100

0.076

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