rs1409004

Variant names:

• chr13-78577102-A-G
• rs1409004
• ENST00000607862.5:n.316-1375A>G

Your query was ambiguous. Multiple possible variants found:

• chr13-78577102-A-G
• chr13-78577102-A-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.316-1375A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,172 control chromosomes in the GnomAD database, including 5,813 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 0.24 (5813 hom., cov: 32)
• Consequence: OBI1-AS1 ENST00000607862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 1 publications found

Genes affected

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

ENSG00000296474 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.456 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.385-28199A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OBI1-AS1	ENST00000607862.5	TSL:1	n.316-1375A>G		intron	N/A
	OBI1-AS1	ENST00000430549.6	TSL:4	n.243-1375A>G		intron	N/A
	OBI1-AS1	ENST00000444769.7	TSL:4	n.217-1375A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35894 AN: 152054 Hom.: 5782 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.236 AC: 35976 AN: 152172 Hom.: 5813 Cov.: 32 AF XY: 0.234 AC XY: 17437 AN XY: 74420

African (AFR) AF: 0.462 AC: 19156 AN: 41486

American (AMR) AF: 0.151 AC: 2302 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 408 AN: 3472

East Asian (EAS) AF: 0.122 AC: 632 AN: 5190

South Asian (SAS) AF: 0.207 AC: 997 AN: 4820

European-Finnish (FIN) AF: 0.154 AC: 1634 AN: 10620

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10161 AN: 67984

Other (OTH) AF: 0.208 AC: 439 AN: 2110

Alfa AF: 0.207 Hom.: 980

Bravo AF: 0.245

Asia WGS AF: 0.210 AC: 730 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.27
DANN	Benign	0.47
PhyloP100		-1.1

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: rs1409004;

hg19: chr13-79151237;