Genetic Variant ENST00000607862.5:n.231-39474C>A (chr13-78234779-C-A) – 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.231-39474C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 151,998 control chromosomes in the GnomAD database, including 14,042 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 0.41 ( 14042 hom., cov: 32)

Consequence

OBI1-AS1
ENST00000607862.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.950

Publications

10 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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OBI1-AS1	NR_047001.1 link	n.300-39474C>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
OBI1-AS1	ENST00000607862.5 link	n.231-39474C>A	intron_variant	Intron 1 of 2	1
OBI1-AS1	ENST00000430549.6 link	n.158-39474C>A	intron_variant	Intron 2 of 4	4
OBI1-AS1	ENST00000444769.7 link	n.132-39474C>A	intron_variant	Intron 2 of 5	4

Frequencies

GnomAD3 genomes

AF:

0.413

AC:

62736

AN:

151880

Hom.:

14015

Cov.:

show subpopulations

Gnomad AFR

AF:

0.528

Gnomad AMI

AF:

0.283

Gnomad AMR

AF:

0.523

Gnomad ASJ

AF:

0.318

Gnomad EAS

AF:

0.685

Gnomad SAS

AF:

0.417

Gnomad FIN

AF:

0.415

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.305

Gnomad OTH

AF:

0.381

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

GnomAD4 genome

AF:

0.413

AC:

62822

AN:

151998

Hom.:

14042

Cov.:

AF XY:

0.424

AC XY:

31492

AN XY:

74296

show subpopulations

African (AFR)

AF:

0.529

AC:

21922

AN:

41478

American (AMR)

AF:

0.524

AC:

7982

AN:

15242

Ashkenazi Jewish (ASJ)

AF:

0.318

AC:

1102

AN:

3468

East Asian (EAS)

AF:

0.685

AC:

3545

AN:

5178

South Asian (SAS)

AF:

0.418

AC:

2016

AN:

4824

European-Finnish (FIN)

AF:

0.415

AC:

4385

AN:

10558

Middle Eastern (MID)

AF:

0.347

AC:

102

AN:

294

European-Non Finnish (NFE)

AF:

0.305

AC:

20705

AN:

67932

Other (OTH)

AF:

0.381

AC:

805

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1813

3625

5438

7250

9063

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

570

1140

1710

2280

2850

<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:

0.345

Hom.:

41478

Bravo

AF:

0.428

Asia WGS

AF:

0.520

AC:

1805

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

4.1

(source)

DANN

Benign

0.59

PhyloP100

0.95

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