Genetic Variant OBI1-AS1:n.231-19618T>C (chr13-78254635-T-C) – 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.231-19618T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 151,252 control chromosomes in the GnomAD database, including 37,705 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 0.71 ( 37705 hom., cov: 31)

Consequence

OBI1-AS1
ENST00000607862.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.466

Publications

3 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 (EAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OBI1-AS1	NR_047001.1 link	n.300-19618T>C		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
OBI1-AS1	ENST00000607862.5 link	n.231-19618T>C	intron_variant	Intron 1 of 2	1
OBI1-AS1	ENST00000430549.6 link	n.158-19618T>C	intron_variant	Intron 2 of 4	4
OBI1-AS1	ENST00000444769.7 link	n.132-19618T>C	intron_variant	Intron 2 of 5	4

Frequencies

GnomAD3 genomes

AF:

0.706

AC:

106653

AN:

151134

Hom.:

37664

Cov.:

show subpopulations

Gnomad AFR

AF:

0.729

Gnomad AMI

AF:

0.823

Gnomad AMR

AF:

0.768

Gnomad ASJ

AF:

0.628

Gnomad EAS

AF:

0.792

Gnomad SAS

AF:

0.764

Gnomad FIN

AF:

0.620

Gnomad MID

AF:

0.799

Gnomad NFE

AF:

0.682

Gnomad OTH

AF:

0.705

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

GnomAD4 genome

AF:

0.706

AC:

106746

AN:

151252

Hom.:

37705

Cov.:

AF XY:

0.708

AC XY:

52254

AN XY:

73820

show subpopulations

African (AFR)

AF:

0.728

AC:

30038

AN:

41252

American (AMR)

AF:

0.768

AC:

11667

AN:

15190

Ashkenazi Jewish (ASJ)

AF:

0.628

AC:

2173

AN:

3462

East Asian (EAS)

AF:

0.793

AC:

4045

AN:

5104

South Asian (SAS)

AF:

0.766

AC:

3684

AN:

4812

European-Finnish (FIN)

AF:

0.620

AC:

6477

AN:

10440

Middle Eastern (MID)

AF:

0.805

AC:

235

AN:

292

European-Non Finnish (NFE)

AF:

0.682

AC:

46199

AN:

67700

Other (OTH)

AF:

0.708

AC:

1482

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1632

3264

4897

6529

8161

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

832

1664

2496

3328

4160

<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:

0.680

Hom.:

4327

Bravo

AF:

0.719

Asia WGS

AF:

0.755

AC:

2621

AN:

3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.89

(source)

DANN

Benign

0.52

PhyloP100

-0.47

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