rs9574199

Variant names:

• chr13-78234779-C-A
• rs9574199
• ENST00000607862.5:n.231-39474C>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000607862.5(OBI1-AS1):​n.231-39474C>A variant causes a intron 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 ENST00000607862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.950
• Publications: 10 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 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.300-39474C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OBI1-AS1	ENST00000607862.5	TSL:1	n.231-39474C>A		intron	N/A
	OBI1-AS1	ENST00000430549.6	TSL:4	n.158-39474C>A		intron	N/A
	OBI1-AS1	ENST00000444769.7	TSL:4	n.132-39474C>A		intron	N/A

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

African (AFR) AF: 0.529 AC: 21922 AN: 41478

American (AMR) AF: 0.524 AC: 7982 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1102 AN: 3468

East Asian (EAS) AF: 0.685 AC: 3545 AN: 5178

South Asian (SAS) AF: 0.418 AC: 2016 AN: 4824

European-Finnish (FIN) AF: 0.415 AC: 4385 AN: 10558

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20705 AN: 67932

Other (OTH) AF: 0.381 AC: 805 AN: 2112

Alfa AF: 0.345 Hom.: 41478

Bravo AF: 0.428

Asia WGS AF: 0.520 AC: 1805 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.1
DANN	Benign	0.59
PhyloP100		0.95

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: rs9574199;

hg19: chr13-78808914;