rs10504337

chr8-61852708-T-C

Variant summary

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

The ENST00000518593.5(LINC02842):n.359T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0218 in 152,296 control chromosomes in the GnomAD database, including 127 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 0.022 (127 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: LINC02842 ENST00000518593.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130

Genes affected

LINC02842 (HGNC:54378): (long intergenic non-protein coding RNA 2842)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0997 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02842	XR_428353.4	n.521T>C		non_coding_transcript_exon_variant	4/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02842	ENST00000518593.5	n.359T>C		non_coding_transcript_exon_variant	3/4	3

Frequencies

GnomAD3 genomes AF: 0.0218 AC: 3312 AN: 152180 Hom.: 125 Cov.: 33

Gnomad AFR AF: 0.00323

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0194

Gnomad FIN AF: 0.0322

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0158

Gnomad OTH AF: 0.0186

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0218 AC: 3318 AN: 152296 Hom.: 127 Cov.: 33 AF XY: 0.0248 AC XY: 1850 AN XY: 74462

Gnomad4 AFR AF: 0.00322

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.00980

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0197

Gnomad4 FIN AF: 0.0322

Gnomad4 NFE AF: 0.0158

Gnomad4 OTH AF: 0.0184

Alfa AF: 0.0217 Hom.: 10

Bravo AF: 0.0254

Asia WGS AF: 0.0120 AC: 40 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.3
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504337; hg19: chr8-62765267;