chr11-130672987-C-T

Variant names:

• chr11-130672987-C-T
• rs7933829
• ENST00000317019.2:n.32C>T

Variant summary

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

The ENST00000317019.2(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 ENST00000317019.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.314
• Publications: 10 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02873	NR_164144.1	n.32C>T		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02873	ENST00000317019.2	n.32C>T		non_coding_transcript_exon_variant	Exon 1 of 3	2
LINC02873	ENST00000721900.1	n.194-40207C>T		intron_variant	Intron 1 of 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

GnomAD2 exomes AF: 0.228 AC: 35258 AN: 154924 AF XY: 0.224

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 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

African (AFR) AF: 0.325 AC: 7912 AN: 24382

American (AMR) AF: 0.206 AC: 5814 AN: 28194

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 3527 AN: 15880

East Asian (EAS) AF: 0.353 AC: 4534 AN: 12834

South Asian (SAS) AF: 0.194 AC: 14748 AN: 76056

European-Finnish (FIN) AF: 0.220 AC: 6249 AN: 28352

Middle Eastern (MID) AF: 0.208 AC: 899 AN: 4330

European-Non Finnish (NFE) AF: 0.211 AC: 193861 AN: 919908

Other (OTH) AF: 0.213 AC: 8850 AN: 41580

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

African (AFR) AF: 0.317 AC: 13140 AN: 41466

American (AMR) AF: 0.223 AC: 3408 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 763 AN: 3468

East Asian (EAS) AF: 0.347 AC: 1785 AN: 5144

South Asian (SAS) AF: 0.193 AC: 931 AN: 4822

European-Finnish (FIN) AF: 0.215 AC: 2274 AN: 10590

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14611 AN: 67990

Other (OTH) AF: 0.244 AC: 515 AN: 2114

Alfa AF: 0.228 Hom.: 19171

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
PhyloP100		0.31
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7933829; hg19: chr11-130542882;