13-78062656-C-T

Position:

• chr13-78062656-C-T

Variant summary

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

The ENST00000607862.5(OBI1-AS1):​n.230+142738C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 151,934 control chromosomes in the GnomAD database, including 38,222 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 (38222 hom., cov: 30)
• Consequence: OBI1-AS1 ENST00000607862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373

Genes affected

OBI1-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OBI1-AS1	NR_047001.1	n.210+7592C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OBI1-AS1	ENST00000607862.5	n.230+142738C>T		intron_variant		1
OBI1-AS1	ENST00000430549.6	n.68+7592C>T		intron_variant		4
OBI1-AS1	ENST00000444769.7	n.42+7592C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.704 AC: 106862 AN: 151818 Hom.: 38216 Cov.: 30

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.704 AC: 106898 AN: 151934 Hom.: 38222 Cov.: 30 AF XY: 0.707 AC XY: 52497 AN XY: 74254

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.745

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.703

Alfa AF: 0.726 Hom.: 83074

Bravo AF: 0.701

Asia WGS AF: 0.820 AC: 2852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	3.9
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2775139; hg19: chr13-78636791;