rs2265775

Positions:

• chr13-78376488-A-C
• chr13-78376488-A-G

Variant summary

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

The ENST00000607862.5(OBI1-AS1):​n.315+102151A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,106 control chromosomes in the GnomAD database, including 24,865 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 0.57 (24865 hom., cov: 32)
• Consequence: OBI1-AS1 ENST00000607862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

OBI1-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OBI1-AS1	NR_047001.1	n.384+102151A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OBI1-AS1	ENST00000607862.5	n.315+102151A>C		intron_variant		1
OBI1-AS1	ENST00000430549.6	n.242+102151A>C		intron_variant		4
OBI1-AS1	ENST00000444769.7	n.216+102151A>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86423 AN: 151988 Hom.: 24842 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.569 AC: 86491 AN: 152106 Hom.: 24865 Cov.: 32 AF XY: 0.573 AC XY: 42578 AN XY: 74344

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.700

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.577

Alfa AF: 0.566 Hom.: 30358

Bravo AF: 0.565

Asia WGS AF: 0.610 AC: 2120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2265775; hg19: chr13-78950623;