chr13-78089389-A-C

Variant names:

• chr13-78089389-A-C
• rs1332944
• ENST00000607862.5:n.230+169471A>C

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+169471A>C variant causes a intron 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 ENST00000607862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530
• 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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 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.210+34325A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OBI1-AS1	ENST00000607862.5	TSL:1	n.230+169471A>C		intron	N/A
	OBI1-AS1	ENST00000430549.6	TSL:4	n.68+34325A>C		intron	N/A
	OBI1-AS1	ENST00000444769.7	TSL:4	n.42+34325A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104212 AN: 151864 Hom.: 37123 Cov.: 31

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

African (AFR) AF: 0.485 AC: 20080 AN: 41434

American (AMR) AF: 0.776 AC: 11831 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2196 AN: 3460

East Asian (EAS) AF: 0.964 AC: 4995 AN: 5180

South Asian (SAS) AF: 0.782 AC: 3765 AN: 4814

European-Finnish (FIN) AF: 0.789 AC: 8331 AN: 10554

Middle Eastern (MID) AF: 0.719 AC: 210 AN: 292

European-Non Finnish (NFE) AF: 0.747 AC: 50761 AN: 67972

Other (OTH) AF: 0.688 AC: 1452 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.4
DANN	Benign	0.91
PhyloP100		0.053

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: rs1332944;

hg19: chr13-78663524;