8-82123474-C-T

Variant names:

• chr8-82123474-C-T
• rs16919670
• ENST00000520155.1:n.154-24354G>A

Variant summary

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

The ENST00000520155.1(LINC02839):​n.154-24354G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,042 control chromosomes in the GnomAD database, including 1,617 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 0.14 (1617 hom., cov: 32)
• Consequence: LINC02839 ENST00000520155.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 3 publications found

Genes affected

LINC02839 (HGNC:54373): (long intergenic non-protein coding RNA 2839)

ENSG00000254394 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02839	NR_183479.1	n.282-14761G>A		intron_variant	Intron 2 of 2
LINC02839	NR_183481.1	n.203-14761G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02839	ENST00000520155.1	n.154-24354G>A		intron_variant	Intron 2 of 2	3
LINC02839	ENST00000520988.2	n.353-14761G>A		intron_variant	Intron 2 of 2	3
LINC02839	ENST00000654599.2	n.249-14761G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20624 AN: 151924 Hom.: 1617 Cov.: 32

Gnomad AFR AF: 0.0829

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.136 AC: 20635 AN: 152042 Hom.: 1617 Cov.: 32 AF XY: 0.134 AC XY: 9938 AN XY: 74310

African (AFR) AF: 0.0830 AC: 3442 AN: 41486

American (AMR) AF: 0.105 AC: 1607 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 498 AN: 3468

East Asian (EAS) AF: 0.290 AC: 1495 AN: 5152

South Asian (SAS) AF: 0.192 AC: 927 AN: 4820

European-Finnish (FIN) AF: 0.123 AC: 1295 AN: 10552

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10884 AN: 67984

Other (OTH) AF: 0.131 AC: 276 AN: 2112

Alfa AF: 0.0849 Hom.: 156

Bravo AF: 0.128

Asia WGS AF: 0.250 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.73
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs16919670; hg19: chr8-83035709;