rs1847461

chr12-90683731-G-Achr12-90683731-G-T

Variant summary

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

The ENST00000652014.1(LINC02822):n.860+3786G>A 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 0.0808 in 151,640 control chromosomes in the GnomAD database, including 795 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 0.081 (795 hom., cov: 32)
• Consequence: LINC02822 ENST00000652014.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189

Genes affected

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

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.354 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
LINC02822	ENST00000652014.1	n.860+3786G>A		intron_variant, non_coding_transcript_variant
	ENST00000670607.1	n.527+19771C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0808 AC: 12239 AN: 151520 Hom.: 791 Cov.: 32

Gnomad AFR AF: 0.0614

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.138

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: 0.0579

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.0808 AC: 12260 AN: 151640 Hom.: 795 Cov.: 32 AF XY: 0.0839 AC XY: 6219 AN XY: 74136

Gnomad4 AFR AF: 0.0617

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0532

Gnomad4 NFE AF: 0.0579

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0743 Hom.: 1187

Bravo AF: 0.0896

Asia WGS AF: 0.199 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.84
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1847461; hg19: chr12-91077508;