13-78287401-C-T

Variant names:

• chr13-78287401-C-T
• rs1324794
• ENST00000607862.5:n.315+13064C>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.315+13064C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 151,624 control chromosomes in the GnomAD database, including 37,705 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 (37705 hom., cov: 32)
• Consequence: OBI1-AS1 ENST00000607862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.476
• Publications: 3 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OBI1-AS1	NR_047001.1	n.384+13064C>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.315+13064C>T		intron_variant	Intron 2 of 2	1
OBI1-AS1	ENST00000430549.6	n.242+13064C>T		intron_variant	Intron 3 of 4	4
OBI1-AS1	ENST00000444769.7	n.216+13064C>T		intron_variant	Intron 3 of 5	4

Frequencies

GnomAD3 genomes AF: 0.705 AC: 106749 AN: 151506 Hom.: 37664 Cov.: 32

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.793

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.705 AC: 106842 AN: 151624 Hom.: 37705 Cov.: 32 AF XY: 0.707 AC XY: 52389 AN XY: 74078

African (AFR) AF: 0.725 AC: 30031 AN: 41420

American (AMR) AF: 0.767 AC: 11660 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2176 AN: 3464

East Asian (EAS) AF: 0.793 AC: 4069 AN: 5128

South Asian (SAS) AF: 0.765 AC: 3691 AN: 4824

European-Finnish (FIN) AF: 0.624 AC: 6582 AN: 10552

Middle Eastern (MID) AF: 0.798 AC: 233 AN: 292

European-Non Finnish (NFE) AF: 0.682 AC: 46162 AN: 67724

Other (OTH) AF: 0.705 AC: 1488 AN: 2110

Alfa AF: 0.646 Hom.: 3540

Bravo AF: 0.717

Asia WGS AF: 0.752 AC: 2608 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.33
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs1324794; hg19: chr13-78861536;