rs620598

Variant names:

• chr6-152799678-A-G
• rs620598
• ENST00000456715.5:n.184-4924T>C

Variant summary

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

The ENST00000456715.5(LINC02840):​n.184-4924T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 151,758 control chromosomes in the GnomAD database, including 4,474 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 0.24 (4474 hom., cov: 32)
• Consequence: LINC02840 ENST00000456715.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456715.5. 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
	LINC02840	NR_183504.1		n.374+32176T>C		intron	N/A
	LINC02840	NR_183505.1		n.590+31375T>C		intron	N/A
	LINC02840	NR_183507.1		n.590+31375T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02840	ENST00000456715.5	TSL:3	n.184-4924T>C		intron	N/A
	LINC02840	ENST00000654424.1		n.558+31375T>C		intron	N/A
	LINC02840	ENST00000656248.1		n.569+31375T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35992 AN: 151640 Hom.: 4474 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.237 AC: 35996 AN: 151758 Hom.: 4474 Cov.: 32 AF XY: 0.236 AC XY: 17492 AN XY: 74198

African (AFR) AF: 0.291 AC: 12078 AN: 41448

American (AMR) AF: 0.177 AC: 2697 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 883 AN: 3458

East Asian (EAS) AF: 0.274 AC: 1409 AN: 5148

South Asian (SAS) AF: 0.223 AC: 1074 AN: 4820

European-Finnish (FIN) AF: 0.197 AC: 2088 AN: 10600

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15168 AN: 67772

Other (OTH) AF: 0.235 AC: 496 AN: 2110

Alfa AF: 0.224 Hom.: 3117

Bravo AF: 0.236

Asia WGS AF: 0.253 AC: 884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.67
PhyloP100		0.29

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: rs620598;

hg19: chr6-153120813;