13-78451652-C-T

Variant names:

• chr13-78451652-C-T
• rs9318552
• ENST00000607862.5:n.316-126825C>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.316-126825C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 151,982 control chromosomes in the GnomAD database, including 9,678 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 0.34 (9678 hom., cov: 33)
• Consequence: OBI1-AS1 ENST00000607862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 7 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 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.385-153649C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OBI1-AS1	ENST00000607862.5	TSL:1	n.316-126825C>T		intron	N/A
	OBI1-AS1	ENST00000430549.6	TSL:4	n.243-126825C>T		intron	N/A
	OBI1-AS1	ENST00000444769.7	TSL:4	n.217-126825C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51056 AN: 151864 Hom.: 9639 Cov.: 33

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.337 AC: 51143 AN: 151982 Hom.: 9678 Cov.: 33 AF XY: 0.342 AC XY: 25396 AN XY: 74282

African (AFR) AF: 0.483 AC: 20010 AN: 41420

American (AMR) AF: 0.389 AC: 5946 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 738 AN: 3472

East Asian (EAS) AF: 0.523 AC: 2700 AN: 5166

South Asian (SAS) AF: 0.263 AC: 1265 AN: 4818

European-Finnish (FIN) AF: 0.338 AC: 3559 AN: 10538

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15990 AN: 67978

Other (OTH) AF: 0.318 AC: 673 AN: 2114

Alfa AF: 0.260 Hom.: 24840

Bravo AF: 0.346

Asia WGS AF: 0.417 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.0
DANN	Benign	0.74
PhyloP100		0.31

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: rs9318552;

hg19: chr13-79025787;