rs546599

Variant names:

• chr6-152797675-C-A
• rs546599
• ENST00000456715.5:n.184-2921G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-152797675-C-A
• chr6-152797675-C-T

Variant summary

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

The ENST00000456715.5(LINC02840):​n.184-2921G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 151,634 control chromosomes in the GnomAD database, including 2,418 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 0.17 (2418 hom., cov: 32)
• Consequence: LINC02840 ENST00000456715.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02840	NR_183504.1	n.374+34179G>T		intron_variant	Intron 2 of 3
LINC02840	NR_183505.1	n.590+33378G>T		intron_variant	Intron 3 of 4
LINC02840	NR_183507.1	n.591-31613G>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02840	ENST00000456715.5	n.184-2921G>T		intron_variant	Intron 2 of 2	3
LINC02840	ENST00000654424.1	n.558+33378G>T		intron_variant	Intron 3 of 4
LINC02840	ENST00000656248.1	n.570-31613G>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26135 AN: 151516 Hom.: 2418 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.00233

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.172 AC: 26128 AN: 151634 Hom.: 2418 Cov.: 32 AF XY: 0.167 AC XY: 12359 AN XY: 74052

African (AFR) AF: 0.154 AC: 6357 AN: 41396

American (AMR) AF: 0.131 AC: 1982 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 796 AN: 3466

East Asian (EAS) AF: 0.00233 AC: 12 AN: 5148

South Asian (SAS) AF: 0.111 AC: 532 AN: 4802

European-Finnish (FIN) AF: 0.159 AC: 1678 AN: 10524

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14306 AN: 67804

Other (OTH) AF: 0.176 AC: 370 AN: 2104

Alfa AF: 0.124 Hom.: 308

Bravo AF: 0.167

Asia WGS AF: 0.0510 AC: 181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.68
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs546599; hg19: chr6-153118810;