8-29773426-G-T

Variant names:

• chr8-29773426-G-T
• rs6982080
• ENST00000517491.1:n.231-16906G>T

Variant summary

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

The ENST00000517491.1(LINC02099):​n.231-16906G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,076 control chromosomes in the GnomAD database, including 17,122 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 0.44 (17122 hom., cov: 32)
• Consequence: LINC02099 ENST00000517491.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 6 publications found

Genes affected

LINC02099 (HGNC:52953): (long intergenic non-protein coding RNA 2099)

ENSG00000304872 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000517491.1. 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
	LINC02099	NR_125814.1		n.272-16906G>T		intron	N/A
	LINC02099	NR_125815.1		n.272-16906G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02099	ENST00000517491.1	TSL:1	n.231-16906G>T		intron	N/A
	LINC02099	ENST00000523123.5	TSL:1	n.256-16906G>T		intron	N/A
	ENSG00000304872	ENST00000806789.1		n.96-30C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66104 AN: 151958 Hom.: 17086 Cov.: 32

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.435 AC: 66193 AN: 152076 Hom.: 17122 Cov.: 32 AF XY: 0.431 AC XY: 32044 AN XY: 74338

African (AFR) AF: 0.732 AC: 30388 AN: 41486

American (AMR) AF: 0.376 AC: 5754 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1226 AN: 3470

East Asian (EAS) AF: 0.166 AC: 857 AN: 5176

South Asian (SAS) AF: 0.325 AC: 1568 AN: 4820

European-Finnish (FIN) AF: 0.343 AC: 3630 AN: 10570

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21403 AN: 67956

Other (OTH) AF: 0.432 AC: 910 AN: 2108

Alfa AF: 0.337 Hom.: 14809

Bravo AF: 0.451

Asia WGS AF: 0.275 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.14
DANN	Benign	0.67
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs6982080; hg19: chr8-29630942;