rs546599

chr6-152797675-C-Achr6-152797675-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_183504.1(LINC02840):n.374+34179G>T variant causes a intron, non coding transcript 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 NR_183504.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02840	NR_183504.1	n.374+34179G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02840	ENST00000666093.1	n.425+33378G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.00233

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.176

Alfa AF: 0.123 Hom.: 298

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs546599; hg19: chr6-153118810;