11-130672987-C-T

Position:

• chr11-130672987-C-T

Variant summary

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

The NR_164144.1(LINC02873):​n.32C>T 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 0.218 in 1,303,604 control chromosomes in the GnomAD database, including 31,909 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 0.25 (4862 hom., cov: 32)
  • Exomes 𝑓: 0.21 (27047 hom.)
• Consequence: LINC02873 NR_164144.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.314

Genes affected

LINC02873 (HGNC:26805): (long intergenic non-protein coding RNA 2873)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02873	NR_164144.1	n.32C>T		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02873	ENST00000317019.2	n.32C>T		non_coding_transcript_exon_variant	1/3	2

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37704 AN: 151968 Hom.: 4864 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.244

GnomAD3 exomes AF: 0.228 AC: 35258 AN: 154924 Hom.: 4241 AF XY: 0.224 AC XY: 18316 AN XY: 81758

Gnomad AFR exome AF: 0.330

Gnomad AMR exome AF: 0.206

Gnomad ASJ exome AF: 0.220

Gnomad EAS exome AF: 0.353

Gnomad SAS exome AF: 0.191

Gnomad FIN exome AF: 0.220

Gnomad NFE exome AF: 0.216

Gnomad OTH exome AF: 0.215

GnomAD4 exome AF: 0.214 AC: 246394 AN: 1151516 Hom.: 27047 Cov.: 31 AF XY: 0.214 AC XY: 120672 AN XY: 564612

Gnomad4 AFR exome AF: 0.325

Gnomad4 AMR exome AF: 0.206

Gnomad4 ASJ exome AF: 0.222

Gnomad4 EAS exome AF: 0.353

Gnomad4 SAS exome AF: 0.194

Gnomad4 FIN exome AF: 0.220

Gnomad4 NFE exome AF: 0.211

Gnomad4 OTH exome AF: 0.213

GnomAD4 genome AF: 0.248 AC: 37726 AN: 152088 Hom.: 4862 Cov.: 32 AF XY: 0.248 AC XY: 18440 AN XY: 74378

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.244

Alfa AF: 0.222 Hom.: 9116

Bravo AF: 0.254

Asia WGS AF: 0.243 AC: 849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7933829; hg19: chr11-130542882;