16-86183013-C-T

Variant names:

• chr16-86183013-C-T
• rs11641863
• ENST00000806579.1:n.173-16499C>T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000806579.1(LINC01082):​n.173-16499C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 152,050 control chromosomes in the GnomAD database, including 27,405 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.59 (27405 hom., cov: 32)
• Consequence: LINC01082 ENST00000806579.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.642
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BP6: Variant 16-86183013-C-T is Benign according to our data. Variant chr16-86183013-C-T is described in ClinVar as Benign. ClinVar VariationId is 1660345.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806579.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01082	ENST00000806579.1		n.173-16499C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90117 AN: 151932 Hom.: 27383 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.593 AC: 90186 AN: 152050 Hom.: 27405 Cov.: 32 AF XY: 0.586 AC XY: 43549 AN XY: 74344

African (AFR) AF: 0.501 AC: 20780 AN: 41440

American (AMR) AF: 0.513 AC: 7841 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2167 AN: 3470

East Asian (EAS) AF: 0.373 AC: 1927 AN: 5172

South Asian (SAS) AF: 0.569 AC: 2745 AN: 4824

European-Finnish (FIN) AF: 0.601 AC: 6346 AN: 10552

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46317 AN: 67996

Other (OTH) AF: 0.600 AC: 1266 AN: 2110

Alfa AF: 0.491 Hom.: 1396

Bravo AF: 0.581

Asia WGS AF: 0.463 AC: 1611 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.50
DANN	Benign	0.34
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs11641863; hg19: chr16-86216619;