6-152809396-C-G

Position:

• chr6-152809396-C-G

Variant summary

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

The NR_183504.1(LINC02840):​n.374+22458G>C 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 0.371 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 NR_183504.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.705

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02840	NR_183504.1	n.374+22458G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02840	ENST00000666093.1	n.425+21657G>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.390

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs484291; hg19: chr6-153130531;