Variant 13-78376801-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000607862.5(OBI1-AS1):n.315+102464C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 151,858 control chromosomes in the GnomAD database, including 24,613 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 0.57 ( 24613 hom., cov: 31)

Consequence

OBI1-AS1
ENST00000607862.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0490

Variant links:

Genes affected

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

OBI1-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OBI1-AS1	NR_047001.1 link	n.384+102464C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
OBI1-AS1	ENST00000607862.5 link	n.315+102464C>T	intron_variant	1
OBI1-AS1	ENST00000430549.6 link	n.242+102464C>T	intron_variant	4
OBI1-AS1	ENST00000444769.7 link	n.216+102464C>T	intron_variant	4

Frequencies

GnomAD3 genomes

AF:

0.566

AC:

85919

AN:

151738

Hom.:

24590

Cov.:

show subpopulations

Gnomad AFR

AF:

0.504

Gnomad AMI

AF:

0.519

Gnomad AMR

AF:

0.622

Gnomad ASJ

AF:

0.596

Gnomad EAS

AF:

0.700

Gnomad SAS

AF:

0.550

Gnomad FIN

AF:

0.675

Gnomad MID

AF:

0.436

Gnomad NFE

AF:

0.565

Gnomad OTH

AF:

0.577

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

GnomAD4 genome

AF:

0.566

AC:

85988

AN:

151858

Hom.:

24613

Cov.:

AF XY:

0.571

AC XY:

42362

AN XY:

74236

show subpopulations

Gnomad4 AFR

AF:

0.505

Gnomad4 AMR

AF:

0.623

Gnomad4 ASJ

AF:

0.596

Gnomad4 EAS

AF:

0.701

Gnomad4 SAS

AF:

0.550

Gnomad4 FIN

AF:

0.675

Gnomad4 NFE

AF:

0.565

Gnomad4 OTH

AF:

0.572

Alfa

AF:

0.542

Hom.:

9069

Bravo

AF:

0.562

Asia WGS

AF:

0.606

AC:

2105

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

1.3

DANN

Benign

0.40

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over