rs6563036

Variant names:

• chr13-78300498-G-A
• rs6563036
• ENST00000607862.5:n.315+26161G>A

Variant summary

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

The ENST00000607862.5(OBI1-AS1):​n.315+26161G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 151,862 control chromosomes in the GnomAD database, including 9,558 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 0.35 (9558 hom., cov: 32)
• Consequence: OBI1-AS1 ENST00000607862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OBI1-AS1	NR_047001.1	n.384+26161G>A		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OBI1-AS1	ENST00000607862.5	n.315+26161G>A		intron_variant	Intron 2 of 2	1
OBI1-AS1	ENST00000430549.6	n.242+26161G>A		intron_variant	Intron 3 of 4	4
OBI1-AS1	ENST00000444769.7	n.216+26161G>A		intron_variant	Intron 3 of 5	4

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53293 AN: 151744 Hom.: 9551 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.351 AC: 53324 AN: 151862 Hom.: 9558 Cov.: 32 AF XY: 0.350 AC XY: 25996 AN XY: 74192

African (AFR) AF: 0.333 AC: 13801 AN: 41440

American (AMR) AF: 0.317 AC: 4827 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1379 AN: 3470

East Asian (EAS) AF: 0.316 AC: 1614 AN: 5114

South Asian (SAS) AF: 0.483 AC: 2328 AN: 4816

European-Finnish (FIN) AF: 0.258 AC: 2733 AN: 10584

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25308 AN: 67906

Other (OTH) AF: 0.371 AC: 781 AN: 2106

Alfa AF: 0.377 Hom.: 18146

Bravo AF: 0.351

Asia WGS AF: 0.405 AC: 1409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.34
DANN	Benign	0.41
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs6563036; hg19: chr13-78874633;