Genetic Variant ENST00000607862.5:n.230+87991C>T (chr13-78007909-C-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.230+87991C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0479 in 152,176 control chromosomes in the GnomAD database, including 230 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 0.048 ( 230 hom., cov: 32)

Consequence

OBI1-AS1
ENST00000607862.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0680

Publications

5 publications found

Variant links:

Genes affected

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

OBI1-AS1 links:

LINC00446 (HGNC:42783): (long intergenic non-protein coding RNA 446)

LINC00446 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 (AMR) allele frequency at 95% confidence interval = 0.0709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
OBI1-AS1	ENST00000607862.5 link	n.230+87991C>T	intron_variant	Intron 1 of 2	1
LINC00446	ENST00000658245.1 link	n.58+9943C>T	intron_variant	Intron 1 of 3
LINC00446	ENST00000659347.1 link	n.43+9943C>T	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.0479

AC:

7282

AN:

152058

Hom.:

230

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0138

Gnomad AMI

AF:

0.0450

Gnomad AMR

AF:

0.0744

Gnomad ASJ

AF:

0.0625

Gnomad EAS

AF:

0.0257

Gnomad SAS

AF:

0.0290

Gnomad FIN

AF:

0.0493

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0649

Gnomad OTH

AF:

0.0455

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

GnomAD4 genome

AF:

0.0479

AC:

7282

AN:

152176

Hom.:

230

Cov.:

AF XY:

0.0481

AC XY:

3576

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.0137

AC:

570

AN:

41534

American (AMR)

AF:

0.0745

AC:

1137

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.0625

AC:

217

AN:

3472

East Asian (EAS)

AF:

0.0259

AC:

134

AN:

5172

South Asian (SAS)

AF:

0.0288

AC:

139

AN:

4822

European-Finnish (FIN)

AF:

0.0493

AC:

523

AN:

10606

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0648

AC:

4409

AN:

67992

Other (OTH)

AF:

0.0450

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

359

719

1078

1438

1797

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

240

320

400

<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:

0.0533

Hom.:

Bravo

AF:

0.0489

Asia WGS

AF:

0.0230

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

3.0

(source)

DANN

Benign

0.76

PhyloP100

0.068

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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