12-90583699-C-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652014.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02822	ENST00000652014.1		n.87+7118C>G		intron	N/A
	LINC02822	ENST00000656065.1		n.180+7118C>G		intron	N/A
	LINC02822	ENST00000658113.2		n.250+7118C>G		intron	N/A

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

African (AFR) AF: 0.675 AC: 27947 AN: 41418

American (AMR) AF: 0.524 AC: 7959 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1186 AN: 3462

East Asian (EAS) AF: 0.534 AC: 2750 AN: 5152

South Asian (SAS) AF: 0.397 AC: 1908 AN: 4812

European-Finnish (FIN) AF: 0.516 AC: 5442 AN: 10554

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.448 AC: 30285 AN: 67662

Other (OTH) AF: 0.468 AC: 983 AN: 2102

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.41
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs2723900; hg19: chr12-90977476;