16-86197744-CGTGTGTGTGTGTGTGTGT-CGTGTGTGTGTGTGTGT

Variant summary

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

The NR_103859.1(LINC01082):n.232+1361_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 0.16 (1972 hom., cov: 0)
• Consequence: LINC01082 NR_103859.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.806

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 (SAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01082	NR_103859.1	n.232+1361_232+1362del		intron_variant, non_coding_transcript_variant
LOC124903743	XR_007065164.1	n.628-567_628-566del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000599841.1	n.25-567_25-566del		intron_variant, non_coding_transcript_variant		4
LINC01082	ENST00000669926.2	n.459+1361_459+1362del		intron_variant, non_coding_transcript_variant
LINC01082	ENST00000601250.1	n.232+1361_232+1362del		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.160 AC: 23564 AN: 147528 Hom.: 1964 Cov.: 0

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.0920

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.160 AC: 23608 AN: 147634 Hom.: 1972 Cov.: 0 AF XY: 0.159 AC XY: 11418 AN XY: 71816

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.0920

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.166

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;