13-78062656-C-T

Variant names:

• chr13-78062656-C-T
• rs2775139
• ENST00000607862.5:n.230+142738C>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.230+142738C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 151,934 control chromosomes in the GnomAD database, including 38,222 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 0.70 (38222 hom., cov: 30)
• Consequence: OBI1-AS1 ENST00000607862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373
• Publications: 8 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=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 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+7592C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OBI1-AS1	ENST00000607862.5	TSL:1	n.230+142738C>T		intron	N/A
	OBI1-AS1	ENST00000430549.6	TSL:4	n.68+7592C>T		intron	N/A
	OBI1-AS1	ENST00000444769.7	TSL:4	n.42+7592C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.704 AC: 106862 AN: 151818 Hom.: 38216 Cov.: 30

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.704 AC: 106898 AN: 151934 Hom.: 38222 Cov.: 30 AF XY: 0.707 AC XY: 52497 AN XY: 74254

African (AFR) AF: 0.586 AC: 24285 AN: 41410

American (AMR) AF: 0.781 AC: 11933 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2175 AN: 3470

East Asian (EAS) AF: 0.943 AC: 4860 AN: 5152

South Asian (SAS) AF: 0.768 AC: 3689 AN: 4802

European-Finnish (FIN) AF: 0.745 AC: 7858 AN: 10550

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.732 AC: 49775 AN: 67958

Other (OTH) AF: 0.703 AC: 1486 AN: 2114

Alfa AF: 0.725 Hom.: 169380

Bravo AF: 0.701

Asia WGS AF: 0.820 AC: 2852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	3.9
DANN	Benign	0.83
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs2775139; hg19: chr13-78636791;