13-78086892-A-G

Variant names:

• chr13-78086892-A-G
• rs2585499
• ENST00000607862.5:n.230+166974A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000607862.5(OBI1-AS1):​n.230+166974A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 152,006 control chromosomes in the GnomAD database, including 37,676 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 (37676 hom., cov: 30)
• Consequence: OBI1-AS1 ENST00000607862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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 rank	MANE	Protein	UniProt
OBI1-AS1	NR_047001.1	n.210+31828A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OBI1-AS1	ENST00000607862.5	n.230+166974A>G		intron_variant	Intron 1 of 2	1
OBI1-AS1	ENST00000430549.6	n.68+31828A>G		intron_variant	Intron 1 of 4	4
OBI1-AS1	ENST00000444769.7	n.42+31828A>G		intron_variant	Intron 1 of 5	4

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105264 AN: 151888 Hom.: 37667 Cov.: 30

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: 0.696

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

GnomAD4 genome AF: 0.693 AC: 105305 AN: 152006 Hom.: 37676 Cov.: 30 AF XY: 0.699 AC XY: 51911 AN XY: 74300

African (AFR) AF: 0.507 AC: 21014 AN: 41438

American (AMR) AF: 0.780 AC: 11906 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2209 AN: 3464

East Asian (EAS) AF: 0.964 AC: 4976 AN: 5160

South Asian (SAS) AF: 0.782 AC: 3768 AN: 4818

European-Finnish (FIN) AF: 0.790 AC: 8355 AN: 10580

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.747 AC: 50773 AN: 67964

Other (OTH) AF: 0.694 AC: 1467 AN: 2114

Alfa AF: 0.674 Hom.: 2439

Bravo AF: 0.683

Asia WGS AF: 0.841 AC: 2924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.73
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs2585499; hg19: chr13-78661027;