13-78088486-T-C

Variant names:

• chr13-78088486-T-C
• rs2775134
• ENST00000607862.5:n.230+168568T>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+168568T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 152,100 control chromosomes in the GnomAD database, including 37,589 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 (37589 hom., cov: 33)
• Consequence: OBI1-AS1 ENST00000607862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.638
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OBI1-AS1	NR_047001.1	n.210+33422T>C		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OBI1-AS1	ENST00000607862.5	n.230+168568T>C		intron_variant	Intron 1 of 2	1
OBI1-AS1	ENST00000430549.6	n.68+33422T>C		intron_variant	Intron 1 of 4	4
OBI1-AS1	ENST00000444769.7	n.42+33422T>C		intron_variant	Intron 1 of 5	4

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105158 AN: 151982 Hom.: 37583 Cov.: 33

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.692 AC: 105190 AN: 152100 Hom.: 37589 Cov.: 33 AF XY: 0.697 AC XY: 51858 AN XY: 74350

African (AFR) AF: 0.505 AC: 20941 AN: 41484

American (AMR) AF: 0.778 AC: 11885 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2201 AN: 3472

East Asian (EAS) AF: 0.964 AC: 4973 AN: 5160

South Asian (SAS) AF: 0.783 AC: 3771 AN: 4816

European-Finnish (FIN) AF: 0.789 AC: 8354 AN: 10582

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.747 AC: 50765 AN: 67998

Other (OTH) AF: 0.693 AC: 1463 AN: 2110

Alfa AF: 0.731 Hom.: 6769

Bravo AF: 0.682

Asia WGS AF: 0.841 AC: 2923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.0
DANN	Benign	0.50
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs2775134; hg19: chr13-78662621;