2-219715563-T-C

Position:

• chr2-219715563-T-C

Variant summary

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

The ENST00000606673.1(LINC02832):​n.119-21891T>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 0.233 in 152,180 control chromosomes in the GnomAD database, including 4,439 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 0.23 (4439 hom., cov: 33)
• Consequence: LINC02832 ENST00000606673.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.949

Genes affected

LINC02832 (HGNC:54366): (long intergenic non-protein coding RNA 2832)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02832	ENST00000606673.1	n.119-21891T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35521 AN: 152062 Hom.: 4440 Cov.: 33

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.246

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.233 AC: 35524 AN: 152180 Hom.: 4439 Cov.: 33 AF XY: 0.232 AC XY: 17243 AN XY: 74400

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.246

Alfa AF: 0.251 Hom.: 811

Bravo AF: 0.229

Asia WGS AF: 0.199 AC: 690 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	14
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2385573; hg19: chr2-220580285;