16-86197744-CGTGTGTGTGTGTGTGTGT-CGTGTGTGTGTGTGT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NR_103859.1(LINC01082):n.232+1359_232+1362del variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.18 (2805 hom., cov: 0)
• Consequence: LINC01082 NR_103859.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

Genes affected

(HGNC:):

LINC01082 (HGNC:49125): (long intergenic non-protein coding RNA 1082)

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01082	NR_103859.1	n.232+1359_232+1362del		intron_variant, non_coding_transcript_variant
LOC124903743	XR_007065164.1	n.628-569_628-566del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000599841.1	n.25-569_25-566del		intron_variant, non_coding_transcript_variant		4
LINC01082	ENST00000669926.2	n.459+1359_459+1362del		intron_variant, non_coding_transcript_variant
LINC01082	ENST00000601250.1	n.232+1359_232+1362del		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.185 AC: 27300 AN: 147750 Hom.: 2805 Cov.: 0

Gnomad AFR AF: 0.0994

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.185 AC: 27306 AN: 147856 Hom.: 2805 Cov.: 0 AF XY: 0.186 AC XY: 13354 AN XY: 71930

Gnomad4 AFR AF: 0.0996

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.177

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs58016760; hg19: chr16-86231350;