rs1408612

chr13-78146048-T-C

Variant summary

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

The NR_047001.1(OBI1-AS1):n.211-43560T>C variant causes a intron, non coding transcript 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 NR_047001.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72

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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OBI1-AS1	NR_047001.1	n.211-43560T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OBI1-AS1	ENST00000607862.5	n.231-128205T>C		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.814

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.643

Gnomad4 OTH AF: 0.582

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	11
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1408612; hg19: chr13-78720183;