rs12720100

Variant names:

• chr13-77976113-G-A
• rs12720100
• ENST00000607862.5:n.230+56195G>A

Variant summary

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

The ENST00000607862.5(OBI1-AS1):​n.230+56195G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,110 control chromosomes in the GnomAD database, including 2,755 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 0.17 (2755 hom., cov: 32)
• Consequence: OBI1-AS1 ENST00000607862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252

Genes affected

OBI1-AS1 (HGNC:42700): (OBI1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OBI1-AS1	ENST00000607862.5	n.230+56195G>A		intron_variant	Intron 1 of 2	1

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26339 AN: 151992 Hom.: 2754 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.173 AC: 26350 AN: 152110 Hom.: 2755 Cov.: 32 AF XY: 0.179 AC XY: 13317 AN XY: 74370

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.169

Alfa AF: 0.162 Hom.: 372

Bravo AF: 0.180

Asia WGS AF: 0.314 AC: 1092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12720100; hg19: chr13-78550248;