16-86197744-CGTGTGTGTGTGTGTGTGT-CGTGTGTGTGTGT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NR_103859.1(LINC01082):n.232+1357_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 0.0094 (23 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.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00941 (1392/147888) while in subpopulation AFR AF= 0.0328 (1303/39736). AF 95% confidence interval is 0.0313. There are 23 homozygotes in gnomad4. There are 706 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 23 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01082	NR_103859.1	n.232+1357_232+1362del		intron_variant, non_coding_transcript_variant
LOC124903743	XR_007065164.1	n.628-571_628-566del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000599841.1	n.25-571_25-566del		intron_variant, non_coding_transcript_variant		4
LINC01082	ENST00000669926.2	n.459+1357_459+1362del		intron_variant, non_coding_transcript_variant
LINC01082	ENST00000601250.1	n.232+1357_232+1362del		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.00938 AC: 1386 AN: 147784 Hom.: 23 Cov.: 0

Gnomad AFR AF: 0.0327

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00368

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00120

Gnomad SAS AF: 0.000438

Gnomad FIN AF: 0.000101

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000253

Gnomad OTH AF: 0.00448

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

GnomAD4 genome AF: 0.00941 AC: 1392 AN: 147888 Hom.: 23 Cov.: 0 AF XY: 0.00981 AC XY: 706 AN XY: 71940

Gnomad4 AFR AF: 0.0328

Gnomad4 AMR AF: 0.00368

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00101

Gnomad4 SAS AF: 0.000439

Gnomad4 FIN AF: 0.000101

Gnomad4 NFE AF: 0.000253

Gnomad4 OTH AF: 0.00443

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;