rs9574199

Positions:

• chr13-78234779-C-A
• chr13-78234779-C-G
• chr13-78234779-C-T

Variant summary

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

The NR_047001.1(OBI1-AS1):​n.300-39474C>A 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 0.413 in 151,998 control chromosomes in the GnomAD database, including 14,042 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 0.41 (14042 hom., cov: 32)
• Consequence: OBI1-AS1 NR_047001.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.950

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OBI1-AS1	NR_047001.1	n.300-39474C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OBI1-AS1	ENST00000607862.5	n.231-39474C>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62736 AN: 151880 Hom.: 14015 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.413 AC: 62822 AN: 151998 Hom.: 14042 Cov.: 32 AF XY: 0.424 AC XY: 31492 AN XY: 74296

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.381

Alfa AF: 0.327 Hom.: 17914

Bravo AF: 0.428

Asia WGS AF: 0.520 AC: 1805 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.1
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: rs9574199; hg19: chr13-78808914;