rs1328814

Positions:

• chr13-78266026-A-G
• chr13-78266026-A-T

Variant summary

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

The ENST00000607862.5(OBI1-AS1):​n.231-8227A>G 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 152,010 control chromosomes in the GnomAD database, including 37,842 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 0.71 (37842 hom., cov: 32)
• Consequence: OBI1-AS1 ENST00000607862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.659

Genes affected

OBI1-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OBI1-AS1	NR_047001.1	n.300-8227A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OBI1-AS1	ENST00000607862.5	n.231-8227A>G		intron_variant		1
OBI1-AS1	ENST00000430549.6	n.158-8227A>G		intron_variant		4
OBI1-AS1	ENST00000444769.7	n.132-8227A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107076 AN: 151892 Hom.: 37800 Cov.: 32

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.705 AC: 107171 AN: 152010 Hom.: 37842 Cov.: 32 AF XY: 0.707 AC XY: 52542 AN XY: 74272

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.794

Gnomad4 SAS AF: 0.746

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.706

Alfa AF: 0.688 Hom.: 16474

Bravo AF: 0.717

Asia WGS AF: 0.739 AC: 2570 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.1
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1328814; hg19: chr13-78840161;