rs1847461

Variant names:

• chr12-90683731-G-A
• rs1847461
• ENST00000656065.1:n.4739G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-90683731-G-A
• chr12-90683731-G-C
• chr12-90683731-G-T

Variant summary

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

The ENST00000656065.1(LINC02822):​n.4739G>A variant causes a non coding transcript exon 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 ENST00000656065.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189

Genes affected

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

ENSG00000288102 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02822	ENST00000656065.1	n.4739G>A		non_coding_transcript_exon_variant	Exon 5 of 5
LINC02822	ENST00000652014.1	n.860+3786G>A		intron_variant	Intron 5 of 5
LINC02822	ENST00000664727.1	n.121+7119G>A		intron_variant	Intron 2 of 5

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;