13-78089389-A-C

Variant summary

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

The NR_047001.1(OBI1-AS1):​n.210+34325A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 151,982 control chromosomes in the GnomAD database, including 37,130 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 0.69 ( 37130 hom., cov: 31)

Consequence

OBI1-AS1
NR_047001.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0530
Variant links:
Genes affected
OBI1-AS1 (HGNC:42700): (OBI1 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OBI1-AS1NR_047001.1 linkuse as main transcriptn.210+34325A>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OBI1-AS1ENST00000607862.5 linkuse as main transcriptn.230+169471A>C intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.686
AC:
104212
AN:
151864
Hom.:
37123
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.485
Gnomad AMI
AF:
0.684
Gnomad AMR
AF:
0.775
Gnomad ASJ
AF:
0.635
Gnomad EAS
AF:
0.964
Gnomad SAS
AF:
0.781
Gnomad FIN
AF:
0.789
Gnomad MID
AF:
0.726
Gnomad NFE
AF:
0.747
Gnomad OTH
AF:
0.689
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.686
AC:
104245
AN:
151982
Hom.:
37130
Cov.:
31
AF XY:
0.692
AC XY:
51413
AN XY:
74264
show subpopulations
Gnomad4 AFR
AF:
0.485
Gnomad4 AMR
AF:
0.776
Gnomad4 ASJ
AF:
0.635
Gnomad4 EAS
AF:
0.964
Gnomad4 SAS
AF:
0.782
Gnomad4 FIN
AF:
0.789
Gnomad4 NFE
AF:
0.747
Gnomad4 OTH
AF:
0.688
Alfa
AF:
0.721
Hom.:
5036
Bravo
AF:
0.675
Asia WGS
AF:
0.838
AC:
2912
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
1.4
DANN
Benign
0.91

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.

Other links and lift over

dbSNP: rs1332944; hg19: chr13-78663524; API