rs10859032

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ENSG00000288102 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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.860+23503G>A		intron_variant	Intron 5 of 5
LINC02822	ENST00000664727.1	n.121+26836G>A		intron_variant	Intron 2 of 5
LINC02822	ENST00000666236.1	n.198+26797G>A		intron_variant	Intron 2 of 4
ENSG00000288102	ENST00000670607.1	n.527+54C>T		intron_variant	Intron 6 of 7

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

Gnomad4 AFR AF: 0.0274

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.0532

Gnomad4 NFE AF: 0.0577

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0627 Hom.: 168

Bravo AF: 0.0786

Asia WGS AF: 0.196 AC: 680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10859032; hg19: chr12-91097225;