13-78409942-G-C

Variant names:

• chr13-78409942-G-C
• rs1986644
• ENST00000607862.5:n.315+135605G>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+135605G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,084 control chromosomes in the GnomAD database, including 6,484 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 0.28 (6484 hom., cov: 33)
• Consequence: OBI1-AS1 ENST00000607862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340
• Publications: 3 publications found

Genes affected

OBI1-AS1 (HGNC:42700): (OBI1 antisense RNA 1)

ENSG00000305909 (HGNC:):

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 = 0.463 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+135605G>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+135605G>C		intron	N/A
	OBI1-AS1	ENST00000430549.6	TSL:4	n.242+135605G>C		intron	N/A
	OBI1-AS1	ENST00000444769.7	TSL:4	n.216+135605G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41990 AN: 151966 Hom.: 6476 Cov.: 33

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.276 AC: 42012 AN: 152084 Hom.: 6484 Cov.: 33 AF XY: 0.287 AC XY: 21343 AN XY: 74350

African (AFR) AF: 0.166 AC: 6911 AN: 41514

American (AMR) AF: 0.419 AC: 6404 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 846 AN: 3472

East Asian (EAS) AF: 0.479 AC: 2474 AN: 5168

South Asian (SAS) AF: 0.345 AC: 1665 AN: 4826

European-Finnish (FIN) AF: 0.349 AC: 3678 AN: 10548

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19015 AN: 67968

Other (OTH) AF: 0.281 AC: 592 AN: 2110

Alfa AF: 0.255 Hom.: 662

Bravo AF: 0.280

Asia WGS AF: 0.353 AC: 1229 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	3.2
DANN	Benign	0.70
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs1986644; hg19: chr13-78984077;