16-86760070-C-G

Variant names:

• chr16-86760070-C-G
• rs299956
• ENST00000803661.1:n.133-1047C>G

Variant summary

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

The ENST00000803661.1(LINC02188):​n.133-1047C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 152,004 control chromosomes in the GnomAD database, including 8,838 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 0.33 (8838 hom., cov: 31)
• Consequence: LINC02188 ENST00000803661.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.31
• Publications: 3 publications found

Genes affected

LINC02188 (HGNC:53050): (long intergenic non-protein coding RNA 2188)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803661.1. 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
	LINC02188	ENST00000803661.1		n.133-1047C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49857 AN: 151884 Hom.: 8832 Cov.: 31

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.328 AC: 49913 AN: 152004 Hom.: 8838 Cov.: 31 AF XY: 0.324 AC XY: 24077 AN XY: 74312

African (AFR) AF: 0.456 AC: 18907 AN: 41428

American (AMR) AF: 0.354 AC: 5400 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 958 AN: 3468

East Asian (EAS) AF: 0.311 AC: 1602 AN: 5146

South Asian (SAS) AF: 0.313 AC: 1507 AN: 4812

European-Finnish (FIN) AF: 0.190 AC: 2017 AN: 10600

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.271 AC: 18406 AN: 67980

Other (OTH) AF: 0.314 AC: 663 AN: 2114

Alfa AF: 0.130 Hom.: 207

Bravo AF: 0.346

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0060
DANN	Benign	0.60
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs299956; hg19: chr16-86793676;