rs9544725

chr13-78155232-A-G

Variant summary

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

The NR_047001.1(OBI1-AS1):n.211-34376A>G 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 0.662 in 152,036 control chromosomes in the GnomAD database, including 34,097 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 0.66 (34097 hom., cov: 32)
• Consequence: OBI1-AS1 NR_047001.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.520

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OBI1-AS1	NR_047001.1	n.211-34376A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OBI1-AS1	ENST00000607862.5	n.231-119021A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100571 AN: 151918 Hom.: 34079 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.662 AC: 100622 AN: 152036 Hom.: 34097 Cov.: 32 AF XY: 0.662 AC XY: 49205 AN XY: 74304

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.747

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.663

Alfa AF: 0.702 Hom.: 77392

Bravo AF: 0.661

Asia WGS AF: 0.681 AC: 2370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.6
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9544725; hg19: chr13-78729367;