rs276992

Variant names:

• chr16-86187097-C-G
• rs276992
• ENST00000806579.1:n.173-12415C>G

Variant summary

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

The ENST00000806579.1(LINC01082):​n.173-12415C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 152,112 control chromosomes in the GnomAD database, including 23,304 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 0.52 (23304 hom., cov: 32)
• Consequence: LINC01082 ENST00000806579.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104
• Publications: 5 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 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.173-12415C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78649 AN: 151994 Hom.: 23261 Cov.: 32

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.518 AC: 78747 AN: 152112 Hom.: 23304 Cov.: 32 AF XY: 0.523 AC XY: 38915 AN XY: 74350

African (AFR) AF: 0.806 AC: 33469 AN: 41530

American (AMR) AF: 0.569 AC: 8702 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1648 AN: 3470

East Asian (EAS) AF: 0.632 AC: 3267 AN: 5172

South Asian (SAS) AF: 0.475 AC: 2286 AN: 4814

European-Finnish (FIN) AF: 0.405 AC: 4286 AN: 10574

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23523 AN: 67936

Other (OTH) AF: 0.520 AC: 1098 AN: 2112

Alfa AF: 0.452 Hom.: 2194

Bravo AF: 0.547

Asia WGS AF: 0.584 AC: 2034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.34
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs276992; hg19: chr16-86220703;