rs12720100

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

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

LINC01069 (HGNC:49109): (long intergenic non-protein coding RNA 1069)

ACMG classification

Our verdict: Benign. The variant received -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
LINC01069	ENST00000724382.1	n.322-3119C>T		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.145 AC: 6039 AN: 41506

American (AMR) AF: 0.239 AC: 3647 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 445 AN: 3472

East Asian (EAS) AF: 0.538 AC: 2773 AN: 5150

South Asian (SAS) AF: 0.253 AC: 1217 AN: 4812

European-Finnish (FIN) AF: 0.172 AC: 1826 AN: 10594

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9948 AN: 67998

Other (OTH) AF: 0.169 AC: 355 AN: 2104

Alfa AF: 0.161 Hom.: 378

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
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs12720100; hg19: chr13-78550248;