13-78451652-C-T

Variant names:

• chr13-78451652-C-T
• rs9318552
• ENST00000607862.5:n.316-126825C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000607862.5(OBI1-AS1):​n.316-126825C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 151,982 control chromosomes in the GnomAD database, including 9,678 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 0.34 (9678 hom., cov: 33)
• Consequence: OBI1-AS1 ENST00000607862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OBI1-AS1	NR_047001.1	n.385-153649C>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OBI1-AS1	ENST00000607862.5	n.316-126825C>T		intron_variant	Intron 2 of 2	1
OBI1-AS1	ENST00000430549.6	n.243-126825C>T		intron_variant	Intron 3 of 4	4
OBI1-AS1	ENST00000444769.7	n.217-126825C>T		intron_variant	Intron 3 of 5	4

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51056 AN: 151864 Hom.: 9639 Cov.: 33

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.337 AC: 51143 AN: 151982 Hom.: 9678 Cov.: 33 AF XY: 0.342 AC XY: 25396 AN XY: 74282

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.318

Alfa AF: 0.240 Hom.: 9525

Bravo AF: 0.346

Asia WGS AF: 0.417 AC: 1449 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	6.0
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9318552; hg19: chr13-79025787;