13-78087104-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_047001.1(OBI1-AS1):n.210+32040T>G 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 0.693 in 151,958 control chromosomes in the GnomAD database, including 37,654 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 (37654 hom., cov: 31)
• Consequence: OBI1-AS1 NR_047001.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OBI1-AS1	NR_047001.1	n.210+32040T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OBI1-AS1	ENST00000607862.5	n.230+167186T>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105217 AN: 151840 Hom.: 37645 Cov.: 31

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.697

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

GnomAD4 genome AF: 0.693 AC: 105258 AN: 151958 Hom.: 37654 Cov.: 31 AF XY: 0.699 AC XY: 51887 AN XY: 74258

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.780

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.964

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.790

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.695

Alfa AF: 0.729 Hom.: 8326

Bravo AF: 0.683

Asia WGS AF: 0.842 AC: 2926 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	1.2
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2585498; hg19: chr13-78661239;