12-90583699-C-G

Variant names:

• chr12-90583699-C-G
• rs2723900
• ENST00000652014.1:n.87+7118C>G

Variant summary

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

The ENST00000652014.1(LINC02822):​n.87+7118C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 151,544 control chromosomes in the GnomAD database, including 21,418 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 0.52 (21418 hom., cov: 32)
• Consequence: LINC02822 ENST00000652014.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.490

Genes affected

LINC02822 (HGNC:54353): (long intergenic non-protein coding RNA 2822)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02822	ENST00000652014.1	n.87+7118C>G		intron_variant	Intron 1 of 5
LINC02822	ENST00000656065.1	n.180+7118C>G		intron_variant	Intron 1 of 4
LINC02822	ENST00000661507.1	n.87+7118C>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.521 AC: 78819 AN: 151426 Hom.: 21386 Cov.: 32

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.521 AC: 78910 AN: 151544 Hom.: 21418 Cov.: 32 AF XY: 0.522 AC XY: 38637 AN XY: 74054

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.468

Alfa AF: 0.330 Hom.: 783

Bravo AF: 0.529

Asia WGS AF: 0.511 AC: 1776 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2723900; hg19: chr12-90977476;