rs17068683

Variant names:

• chr13-77994736-G-A
• rs17068683
• ENST00000607862.5:n.230+74818G>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.230+74818G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0485 in 152,070 control chromosomes in the GnomAD database, including 231 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 0.048 (231 hom., cov: 32)
• Consequence: OBI1-AS1 ENST00000607862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199
• Publications: 4 publications found

Genes affected

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

LINC01069 (HGNC:49109): (long intergenic non-protein coding RNA 1069)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01069	NR_108076.1	n.38C>T		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OBI1-AS1	ENST00000607862.5	n.230+74818G>A		intron_variant	Intron 1 of 2	1
LINC01069	ENST00000452933.2	n.29+3080C>T		intron_variant	Intron 1 of 4	5
LINC01069	ENST00000662401.1	n.66+3080C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0485 AC: 7365 AN: 151952 Hom.: 231 Cov.: 32

Gnomad AFR AF: 0.0135

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0740

Gnomad ASJ AF: 0.0623

Gnomad EAS AF: 0.0263

Gnomad SAS AF: 0.0483

Gnomad FIN AF: 0.0494

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0649

Gnomad OTH AF: 0.0465

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

GnomAD4 genome AF: 0.0485 AC: 7369 AN: 152070 Hom.: 231 Cov.: 32 AF XY: 0.0490 AC XY: 3644 AN XY: 74318

African (AFR) AF: 0.0135 AC: 560 AN: 41490

American (AMR) AF: 0.0741 AC: 1132 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0623 AC: 216 AN: 3466

East Asian (EAS) AF: 0.0265 AC: 137 AN: 5168

South Asian (SAS) AF: 0.0490 AC: 236 AN: 4816

European-Finnish (FIN) AF: 0.0494 AC: 522 AN: 10560

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0649 AC: 4411 AN: 67982

Other (OTH) AF: 0.0460 AC: 97 AN: 2110

Alfa AF: 0.0607 Hom.: 393

Bravo AF: 0.0488

Asia WGS AF: 0.0330 AC: 115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.45
PhyloP100		0.20
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17068683; hg19: chr13-78568871;