rs276990

Variant names:

• chr16-86187610-A-G
• rs276990
• ENST00000806579.1:n.173-11902A>G

Variant summary

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

The ENST00000806579.1(LINC01082):​n.173-11902A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 151,958 control chromosomes in the GnomAD database, including 24,443 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 0.53 (24443 hom., cov: 32)
• Consequence: LINC01082 ENST00000806579.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930
• 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 (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01082	ENST00000806579.1	n.173-11902A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80200 AN: 151840 Hom.: 24392 Cov.: 32

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.528 AC: 80309 AN: 151958 Hom.: 24443 Cov.: 32 AF XY: 0.534 AC XY: 39607 AN XY: 74230

African (AFR) AF: 0.835 AC: 34655 AN: 41502

American (AMR) AF: 0.575 AC: 8780 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1667 AN: 3470

East Asian (EAS) AF: 0.636 AC: 3265 AN: 5134

South Asian (SAS) AF: 0.469 AC: 2251 AN: 4796

European-Finnish (FIN) AF: 0.407 AC: 4292 AN: 10546

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23810 AN: 67938

Other (OTH) AF: 0.531 AC: 1118 AN: 2106

Alfa AF: 0.403 Hom.: 7190

Bravo AF: 0.560

Asia WGS AF: 0.586 AC: 2041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.44
PhyloP100		-0.093

Splicing

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

Other links and lift over

dbSNP: rs276990; hg19: chr16-86221216;