3-82094500-G-T

Variant names:

• chr3-82094500-G-T
• rs9309886
• ENST00000470263.5:n.245-90852G>T

Variant summary

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

The ENST00000470263.5(LINC02008):​n.245-90852G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 151,948 control chromosomes in the GnomAD database, including 8,819 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 0.29 (8819 hom., cov: 32)
• Consequence: LINC02008 ENST00000470263.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279
• Publications: 1 publications found

Genes affected

LINC02008 (HGNC:52844): (long intergenic non-protein coding RNA 2008)

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 = 0.569 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000470263.5. 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
	LINC02008	NR_147146.1		n.241-90852G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02008	ENST00000470263.5	TSL:1	n.245-90852G>T		intron	N/A
	LINC02008	ENST00000494340.3	TSL:2	n.306+51710G>T		intron	N/A
	LINC02008	ENST00000653255.1		n.326+23634G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43887 AN: 151828 Hom.: 8797 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.289 AC: 43952 AN: 151948 Hom.: 8819 Cov.: 32 AF XY: 0.280 AC XY: 20785 AN XY: 74276

African (AFR) AF: 0.576 AC: 23860 AN: 41452

American (AMR) AF: 0.208 AC: 3174 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 489 AN: 3468

East Asian (EAS) AF: 0.149 AC: 772 AN: 5176

South Asian (SAS) AF: 0.137 AC: 659 AN: 4824

European-Finnish (FIN) AF: 0.121 AC: 1281 AN: 10568

Middle Eastern (MID) AF: 0.202 AC: 59 AN: 292

European-Non Finnish (NFE) AF: 0.190 AC: 12922 AN: 67866

Other (OTH) AF: 0.264 AC: 556 AN: 2110

Alfa AF: 0.177 Hom.: 1335

Bravo AF: 0.309

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.90
DANN	Benign	0.66
PhyloP100		-0.28

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9309886;

hg19: chr3-82143651;