13-78254635-T-C

Variant names:

• chr13-78254635-T-C
• rs1159488
• ENST00000607862.5:n.231-19618T>C

Variant summary

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

The ENST00000607862.5(OBI1-AS1):​n.231-19618T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 151,252 control chromosomes in the GnomAD database, including 37,705 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 0.71 (37705 hom., cov: 31)
• Consequence: OBI1-AS1 ENST00000607862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.466
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.772 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.300-19618T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OBI1-AS1	ENST00000607862.5	TSL:1	n.231-19618T>C		intron	N/A
	OBI1-AS1	ENST00000430549.6	TSL:4	n.158-19618T>C		intron	N/A
	OBI1-AS1	ENST00000444769.7	TSL:4	n.132-19618T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.706 AC: 106653 AN: 151134 Hom.: 37664 Cov.: 31

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.706 AC: 106746 AN: 151252 Hom.: 37705 Cov.: 31 AF XY: 0.708 AC XY: 52254 AN XY: 73820

African (AFR) AF: 0.728 AC: 30038 AN: 41252

American (AMR) AF: 0.768 AC: 11667 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2173 AN: 3462

East Asian (EAS) AF: 0.793 AC: 4045 AN: 5104

South Asian (SAS) AF: 0.766 AC: 3684 AN: 4812

European-Finnish (FIN) AF: 0.620 AC: 6477 AN: 10440

Middle Eastern (MID) AF: 0.805 AC: 235 AN: 292

European-Non Finnish (NFE) AF: 0.682 AC: 46199 AN: 67700

Other (OTH) AF: 0.708 AC: 1482 AN: 2094

Alfa AF: 0.680 Hom.: 4327

Bravo AF: 0.719

Asia WGS AF: 0.755 AC: 2621 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.89
DANN	Benign	0.52
PhyloP100		-0.47

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: rs1159488;

hg19: chr13-78828770;