13-78378213-T-C

Variant names:

• chr13-78378213-T-C
• rs2247058
• ENST00000607862.5:n.315+103876T>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.315+103876T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 152,082 control chromosomes in the GnomAD database, including 27,644 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 0.60 (27644 hom., cov: 33)
• Consequence: OBI1-AS1 ENST00000607862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.460
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.683 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OBI1-AS1	NR_047001.1		n.384+103876T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OBI1-AS1	ENST00000607862.5	TSL:1	n.315+103876T>C		intron	N/A
	OBI1-AS1	ENST00000430549.6	TSL:4	n.242+103876T>C		intron	N/A
	OBI1-AS1	ENST00000444769.7	TSL:4	n.216+103876T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91213 AN: 151960 Hom.: 27612 Cov.: 33

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.600 AC: 91293 AN: 152082 Hom.: 27644 Cov.: 33 AF XY: 0.604 AC XY: 44866 AN XY: 74332

African (AFR) AF: 0.611 AC: 25352 AN: 41494

American (AMR) AF: 0.641 AC: 9789 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2111 AN: 3470

East Asian (EAS) AF: 0.702 AC: 3626 AN: 5168

South Asian (SAS) AF: 0.566 AC: 2731 AN: 4826

European-Finnish (FIN) AF: 0.674 AC: 7114 AN: 10552

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38698 AN: 67978

Other (OTH) AF: 0.599 AC: 1265 AN: 2112

Alfa AF: 0.592 Hom.: 7068

Bravo AF: 0.601

Asia WGS AF: 0.618 AC: 2147 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.41
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs2247058; hg19: chr13-78952348;