16-86197744-CGTGTGTGTGTGTGTGTGT-CGTGTGTGTGTGTGTGTGTGTGT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NR_103859.1(LINC01082):n.232+1359_232+1362dup 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 0.0047 (4 hom., cov: 0)
• Consequence: LINC01082 NR_103859.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAd at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01082	NR_103859.1	n.232+1359_232+1362dup		intron_variant, non_coding_transcript_variant
LOC124903743	XR_007065164.1	n.628-566_628-565insACAC		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000599841.1	n.25-566_25-565insACAC		intron_variant, non_coding_transcript_variant		4
LINC01082	ENST00000669926.2	n.459+1359_459+1362dup		intron_variant, non_coding_transcript_variant
LINC01082	ENST00000601250.1	n.232+1359_232+1362dup		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.00469 AC: 693 AN: 147852 Hom.: 4 Cov.: 0

Gnomad AFR AF: 0.00616

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00281

Gnomad ASJ AF: 0.000292

Gnomad EAS AF: 0.00140

Gnomad SAS AF: 0.00986

Gnomad FIN AF: 0.00513

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00441

Gnomad OTH AF: 0.00348

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

GnomAD4 genome AF: 0.00468 AC: 693 AN: 147958 Hom.: 4 Cov.: 0 AF XY: 0.00472 AC XY: 340 AN XY: 71980

Gnomad4 AFR AF: 0.00614

Gnomad4 AMR AF: 0.00281

Gnomad4 ASJ AF: 0.000292

Gnomad4 EAS AF: 0.00141

Gnomad4 SAS AF: 0.00987

Gnomad4 FIN AF: 0.00513

Gnomad4 NFE AF: 0.00441

Gnomad4 OTH AF: 0.00344

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;