rs1408612

Variant names:

• chr13-78146048-T-C
• rs1408612
• ENST00000607862.5:n.231-128205T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000607862.5(OBI1-AS1):​n.231-128205T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 151,878 control chromosomes in the GnomAD database, including 26,440 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 (26440 hom., cov: 32)
• Consequence: OBI1-AS1 ENST00000607862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607862.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OBI1-AS1	NR_047001.1		n.211-43560T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OBI1-AS1	ENST00000607862.5	TSL:1	n.231-128205T>C		intron	N/A
	OBI1-AS1	ENST00000430549.6	TSL:4	n.69-43560T>C		intron	N/A
	OBI1-AS1	ENST00000444769.7	TSL:4	n.43-43560T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86912 AN: 151758 Hom.: 26426 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.572 AC: 86946 AN: 151878 Hom.: 26440 Cov.: 32 AF XY: 0.576 AC XY: 42783 AN XY: 74252

African (AFR) AF: 0.358 AC: 14844 AN: 41450

American (AMR) AF: 0.691 AC: 10542 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1974 AN: 3470

East Asian (EAS) AF: 0.814 AC: 4211 AN: 5172

South Asian (SAS) AF: 0.616 AC: 2972 AN: 4828

European-Finnish (FIN) AF: 0.652 AC: 6882 AN: 10554

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.643 AC: 43614 AN: 67828

Other (OTH) AF: 0.582 AC: 1227 AN: 2108

Alfa AF: 0.596 Hom.: 3463

Bravo AF: 0.571

Asia WGS AF: 0.665 AC: 2311 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.84
PhyloP100		1.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1408612;

hg19: chr13-78720183;