13-78108728-T-G

Variant names:

• chr13-78108728-T-G
• rs1360367
• ENST00000607862.5:n.231-165525T>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.231-165525T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,910 control chromosomes in the GnomAD database, including 21,378 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 0.53 (21378 hom., cov: 31)
• Consequence: OBI1-AS1 ENST00000607862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.562 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+53664T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OBI1-AS1	ENST00000607862.5	TSL:1	n.231-165525T>G		intron	N/A
	OBI1-AS1	ENST00000430549.6	TSL:4	n.68+53664T>G		intron	N/A
	OBI1-AS1	ENST00000444769.7	TSL:4	n.42+53664T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80029 AN: 151792 Hom.: 21367 Cov.: 31

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.527 AC: 80070 AN: 151910 Hom.: 21378 Cov.: 31 AF XY: 0.525 AC XY: 38986 AN XY: 74258

African (AFR) AF: 0.481 AC: 19932 AN: 41424

American (AMR) AF: 0.455 AC: 6931 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1912 AN: 3464

East Asian (EAS) AF: 0.579 AC: 2992 AN: 5166

South Asian (SAS) AF: 0.501 AC: 2410 AN: 4812

European-Finnish (FIN) AF: 0.582 AC: 6136 AN: 10544

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38064 AN: 67936

Other (OTH) AF: 0.540 AC: 1139 AN: 2110

Alfa AF: 0.546 Hom.: 12427

Bravo AF: 0.518

Asia WGS AF: 0.504 AC: 1753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.65
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1360367; hg19: chr13-78682863;