ENST00000417654.2:n.364-4268G>C

Variant names:

• chr6-152809396-C-G
• rs484291
• ENST00000417654.2:n.364-4268G>C

Variant summary

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

The ENST00000417654.2(LINC02840):​n.364-4268G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 151,778 control chromosomes in the GnomAD database, including 11,216 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 0.37 (11216 hom., cov: 32)
• Consequence: LINC02840 ENST00000417654.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.705
• Publications: 2 publications found

Genes affected

LINC02840 (HGNC:54374): (long intergenic non-protein coding RNA 2840)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417654.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02840	NR_183504.1		n.374+22458G>C		intron	N/A
	LINC02840	NR_183505.1		n.590+21657G>C		intron	N/A
	LINC02840	NR_183507.1		n.590+21657G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02840	ENST00000417654.2	TSL:3	n.364-4268G>C		intron	N/A
	LINC02840	ENST00000456715.5	TSL:3	n.61-4268G>C		intron	N/A
	LINC02840	ENST00000654424.1		n.558+21657G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56310 AN: 151660 Hom.: 11205 Cov.: 32

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.371 AC: 56355 AN: 151778 Hom.: 11216 Cov.: 32 AF XY: 0.365 AC XY: 27078 AN XY: 74156

African (AFR) AF: 0.513 AC: 21244 AN: 41388

American (AMR) AF: 0.288 AC: 4393 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1565 AN: 3462

East Asian (EAS) AF: 0.274 AC: 1410 AN: 5150

South Asian (SAS) AF: 0.293 AC: 1410 AN: 4806

European-Finnish (FIN) AF: 0.251 AC: 2635 AN: 10492

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22610 AN: 67900

Other (OTH) AF: 0.390 AC: 822 AN: 2108

Alfa AF: 0.359 Hom.: 1297

Bravo AF: 0.378

Asia WGS AF: 0.326 AC: 1136 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.38
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs484291; hg19: chr6-153130531;