dbSNP rs35712557: OBI1:c.639-3495_639-3494delTC (chr13-78620615-TGA-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_024546.4(OBI1):c.639-3495_639-3494delTC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 455,938 control chromosomes in the GnomAD database, including 29,606 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.36 ( 10253 hom., cov: 0)

Exomes 𝑓: 0.35 ( 19353 hom. )

Consequence

OBI1
NM_024546.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

Publications

3 publications found

Variant links:

Genes affected

OBI1 (HGNC:20308): (ORC ubiquitin ligase 1) Enables chromatin binding activity and ubiquitin-protein transferase activity. Involved in protein autoubiquitination; protein monoubiquitination; and regulation of DNA replication. Located in chromatin. [provided by Alliance of Genome Resources, Apr 2022]

OBI1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024546.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OBI1	NM_024546.4	MANE Select	c.639-3495_639-3494delTC		intron	N/A	NP_078822.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
OBI1	ENST00000282003.7	TSL:1 MANE Select	c.639-3495_639-3494delTC	intron	N/A	ENSP00000282003.6	Q5W0B1
OBI1	ENST00000916103.1		c.636-3495_636-3494delTC	intron	N/A	ENSP00000586162.1
OBI1	ENST00000880927.1		c.534-3495_534-3494delTC	intron	N/A	ENSP00000550986.1

Frequencies

GnomAD3 genomes

AF:

0.362

AC:

54897

AN:

151694

Hom.:

10238

Cov.:

show subpopulations

Gnomad AFR

AF:

0.371

Gnomad AMI

AF:

0.256

Gnomad AMR

AF:

0.279

Gnomad ASJ

AF:

0.224

Gnomad EAS

AF:

0.371

Gnomad SAS

AF:

0.350

Gnomad FIN

AF:

0.550

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.356

Gnomad OTH

AF:

0.316

GnomAD2 exomes

AF:

0.331

AC:

44438

AN:

134108

AF XY:

0.335

show subpopulations

Gnomad AFR exome

AF:

0.372

Gnomad AMR exome

AF:

0.237

Gnomad ASJ exome

AF:

0.230

Gnomad EAS exome

AF:

0.372

Gnomad FIN exome

AF:

0.543

Gnomad NFE exome

AF:

0.350

Gnomad OTH exome

AF:

0.307

GnomAD4 exome

AF:

0.350

AC:

106558

AN:

304126

Hom.:

19353

AF XY:

0.350

AC XY:

60639

AN XY:

173178

show subpopulations

African (AFR)

AF:

0.375

AC:

3227

AN:

8600

American (AMR)

AF:

0.236

AC:

6441

AN:

27242

Ashkenazi Jewish (ASJ)

AF:

0.230

AC:

2475

AN:

10778

East Asian (EAS)

AF:

0.366

AC:

3366

AN:

9200

South Asian (SAS)

AF:

0.350

AC:

20896

AN:

59674

European-Finnish (FIN)

AF:

0.531

AC:

6787

AN:

12780

Middle Eastern (MID)

AF:

0.255

AC:

708

AN:

2776

European-Non Finnish (NFE)

AF:

0.363

AC:

57657

AN:

158856

Other (OTH)

AF:

0.352

AC:

5001

AN:

14220

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

3211

6422

9633

12844

16055

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

356

712

1068

1424

1780

<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:

0.362

AC:

54951

AN:

151812

Hom.:

10253

Cov.:

AF XY:

0.368

AC XY:

27295

AN XY:

74204

show subpopulations

African (AFR)

AF:

0.371

AC:

15351

AN:

41388

American (AMR)

AF:

0.279

AC:

4262

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.224

AC:

775

AN:

3466

East Asian (EAS)

AF:

0.371

AC:

1910

AN:

5150

South Asian (SAS)

AF:

0.351

AC:

1686

AN:

4804

European-Finnish (FIN)

AF:

0.550

AC:

5771

AN:

10490

Middle Eastern (MID)

AF:

0.286

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.356

AC:

24208

AN:

67916

Other (OTH)

AF:

0.319

AC:

672

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1737

3474

5210

6947

8684

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

536

1072

1608

2144

2680

<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:

0.342

Hom.:

1631

Bravo

AF:

0.343

Asia WGS

AF:

0.387

AC:

1350

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over