rs10859032

Variant names:

• chr12-90703448-G-A
• rs10859032
• ENST00000652014.1:n.860+23503G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000652014.1(LINC02822):​n.860+23503G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.071 in 152,162 control chromosomes in the GnomAD database, including 721 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 0.071 (721 hom., cov: 32)
• Consequence: LINC02822 ENST00000652014.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32
• Publications: 1 publications found

Genes affected

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

ENSG00000288102 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.355 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02822	ENST00000652014.1		n.860+23503G>A		intron	N/A
	LINC02822	ENST00000664727.1		n.121+26836G>A		intron	N/A
	LINC02822	ENST00000666236.1		n.198+26797G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0710 AC: 10794 AN: 152042 Hom.: 718 Cov.: 32

Gnomad AFR AF: 0.0274

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0577

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0710 AC: 10797 AN: 152162 Hom.: 721 Cov.: 32 AF XY: 0.0746 AC XY: 5553 AN XY: 74402

African (AFR) AF: 0.0274 AC: 1139 AN: 41518

American (AMR) AF: 0.134 AC: 2050 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 434 AN: 3468

East Asian (EAS) AF: 0.368 AC: 1904 AN: 5168

South Asian (SAS) AF: 0.100 AC: 484 AN: 4820

European-Finnish (FIN) AF: 0.0532 AC: 564 AN: 10610

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0577 AC: 3924 AN: 68000

Other (OTH) AF: 0.101 AC: 213 AN: 2106

Alfa AF: 0.0626 Hom.: 190

Bravo AF: 0.0786

Asia WGS AF: 0.196 AC: 680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	18
DANN	Benign	0.48
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs10859032; hg19: chr12-91097225;