chr16-86154021-G-A

Variant names:

• chr16-86154021-G-A
• rs2352934
• ENST00000806580.1:n.131+2540G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000806580.1(LINC01082):​n.131+2540G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 152,050 control chromosomes in the GnomAD database, including 13,475 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.42 (13475 hom., cov: 33)
• Consequence: LINC01082 ENST00000806580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.931
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806580.1. 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	ENST00000806580.1		n.131+2540G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63462 AN: 151932 Hom.: 13463 Cov.: 33

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.418 AC: 63511 AN: 152050 Hom.: 13475 Cov.: 33 AF XY: 0.414 AC XY: 30799 AN XY: 74328

African (AFR) AF: 0.475 AC: 19713 AN: 41462

American (AMR) AF: 0.493 AC: 7530 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1416 AN: 3468

East Asian (EAS) AF: 0.243 AC: 1253 AN: 5158

South Asian (SAS) AF: 0.368 AC: 1774 AN: 4822

European-Finnish (FIN) AF: 0.321 AC: 3393 AN: 10582

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.399 AC: 27126 AN: 67966

Other (OTH) AF: 0.411 AC: 868 AN: 2110

Alfa AF: 0.403 Hom.: 19208

Bravo AF: 0.431

Asia WGS AF: 0.370 AC: 1288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.89
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs2352934; hg19: chr16-86187627; COSMIC: COSV74071707;