rs1328814

Variant names:

• chr13-78266026-A-G
• rs1328814
• ENST00000607862.5:n.231-8227A>G

Your query was ambiguous. Multiple possible variants found:

• chr13-78266026-A-G
• chr13-78266026-A-T

Variant summary

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

The ENST00000607862.5(OBI1-AS1):​n.231-8227A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 152,010 control chromosomes in the GnomAD database, including 37,842 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 (37842 hom., cov: 32)
• Consequence: OBI1-AS1 ENST00000607862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.659
• Publications: 1 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607862.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OBI1-AS1	NR_047001.1		n.300-8227A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OBI1-AS1	ENST00000607862.5	TSL:1	n.231-8227A>G		intron	N/A
	OBI1-AS1	ENST00000430549.6	TSL:4	n.158-8227A>G		intron	N/A
	OBI1-AS1	ENST00000444769.7	TSL:4	n.132-8227A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107076 AN: 151892 Hom.: 37800 Cov.: 32

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.705 AC: 107171 AN: 152010 Hom.: 37842 Cov.: 32 AF XY: 0.707 AC XY: 52542 AN XY: 74272

African (AFR) AF: 0.726 AC: 30123 AN: 41482

American (AMR) AF: 0.767 AC: 11692 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2178 AN: 3468

East Asian (EAS) AF: 0.794 AC: 4098 AN: 5158

South Asian (SAS) AF: 0.746 AC: 3585 AN: 4806

European-Finnish (FIN) AF: 0.625 AC: 6604 AN: 10564

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46413 AN: 67966

Other (OTH) AF: 0.706 AC: 1493 AN: 2114

Alfa AF: 0.689 Hom.: 18537

Bravo AF: 0.717

Asia WGS AF: 0.739 AC: 2570 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.1
DANN	Benign	0.77
PhyloP100		0.66

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1328814;

hg19: chr13-78840161;