rs17068683

chr13-77994736-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_108076.1(LINC01069):n.38C>T variant causes a non coding transcript exon 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: LINC01069 NR_108076.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01069	NR_108076.1	n.38C>T		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OBI1-AS1	ENST00000607862.5	n.230+74818G>A		intron_variant, non_coding_transcript_variant		1
LINC01069	ENST00000665945.1	n.66+3080C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0135

Gnomad4 AMR AF: 0.0741

Gnomad4 ASJ AF: 0.0623

Gnomad4 EAS AF: 0.0265

Gnomad4 SAS AF: 0.0490

Gnomad4 FIN AF: 0.0494

Gnomad4 NFE AF: 0.0649

Gnomad4 OTH AF: 0.0460

Alfa AF: 0.0544 Hom.: 33

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17068683; hg19: chr13-78568871;