6-152764099-A-G

Variant names:

• chr6-152764099-A-G
• rs671330
• ENST00000654424.1:n.559-4015T>C

Variant summary

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

The ENST00000654424.1(LINC02840):​n.559-4015T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 151,820 control chromosomes in the GnomAD database, including 37,589 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 0.70 (37589 hom., cov: 30)
• Consequence: LINC02840 ENST00000654424.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654424.1. 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.375-4015T>C		intron	N/A
	LINC02840	NR_183505.1		n.591-4015T>C		intron	N/A
	LINC02840	NR_183507.1		n.665+1889T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02840	ENST00000654424.1		n.559-4015T>C		intron	N/A
	LINC02840	ENST00000656248.1		n.644+1889T>C		intron	N/A
	LINC02840	ENST00000657202.1		n.441+1889T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106110 AN: 151700 Hom.: 37547 Cov.: 30

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.676

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.700 AC: 106201 AN: 151820 Hom.: 37589 Cov.: 30 AF XY: 0.698 AC XY: 51796 AN XY: 74160

African (AFR) AF: 0.816 AC: 33810 AN: 41436

American (AMR) AF: 0.610 AC: 9286 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2430 AN: 3472

East Asian (EAS) AF: 0.835 AC: 4285 AN: 5130

South Asian (SAS) AF: 0.645 AC: 3094 AN: 4796

European-Finnish (FIN) AF: 0.655 AC: 6875 AN: 10500

Middle Eastern (MID) AF: 0.664 AC: 194 AN: 292

European-Non Finnish (NFE) AF: 0.650 AC: 44176 AN: 67946

Other (OTH) AF: 0.681 AC: 1436 AN: 2110

Alfa AF: 0.660 Hom.: 73072

Bravo AF: 0.703

Asia WGS AF: 0.720 AC: 2507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.52
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs671330; hg19: chr6-153085234;