13-77990531-A-G

Position:

• chr13-77990531-A-G

Variant summary

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

The NR_108076.1(LINC01069):​n.160-923T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,046 control chromosomes in the GnomAD database, including 3,711 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 0.20 (3711 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC01069 NR_108076.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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 = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01069	NR_108076.1	n.160-923T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OBI1-AS1	ENST00000607862.5	n.230+70613A>G		intron_variant, non_coding_transcript_variant		1
LINC01069	ENST00000665945.1	n.67-923T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31004 AN: 151928 Hom.: 3703 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.197

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.204 AC: 31044 AN: 152046 Hom.: 3711 Cov.: 32 AF XY: 0.209 AC XY: 15505 AN XY: 74308

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.195

Alfa AF: 0.166 Hom.: 293

Bravo AF: 0.215

Asia WGS AF: 0.329 AC: 1140 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.22
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4884082; hg19: chr13-78564666;