13-78331108-G-T

Position:

• chr13-78331108-G-T

Variant summary

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

The ENST00000607862.5(OBI1-AS1):​n.315+56771G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 152,016 control chromosomes in the GnomAD database, including 31,825 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 0.64 (31825 hom., cov: 33)
• Consequence: OBI1-AS1 ENST00000607862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

Genes affected

OBI1-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OBI1-AS1	NR_047001.1	n.384+56771G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OBI1-AS1	ENST00000607862.5	n.315+56771G>T		intron_variant		1
OBI1-AS1	ENST00000430549.6	n.242+56771G>T		intron_variant		4
OBI1-AS1	ENST00000444769.7	n.216+56771G>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97731 AN: 151898 Hom.: 31783 Cov.: 33

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.644 AC: 97824 AN: 152016 Hom.: 31825 Cov.: 33 AF XY: 0.645 AC XY: 47936 AN XY: 74298

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.684

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.630

Alfa AF: 0.583 Hom.: 10457

Bravo AF: 0.647

Asia WGS AF: 0.590 AC: 2048 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.99
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2248525; hg19: chr13-78905243;