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. The variant received -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
• Publications: 7 publications found

Genes affected

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

ENSG00000288102 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656065.1. 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	ENST00000656065.1		n.4739G>A		non_coding_transcript_exon	Exon 5 of 5
	LINC02822	ENST00000652014.1		n.860+3786G>A		intron	N/A
	LINC02822	ENST00000664727.1		n.121+7119G>A		intron	N/A

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

African (AFR) AF: 0.0617 AC: 2556 AN: 41444

American (AMR) AF: 0.138 AC: 2094 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 431 AN: 3460

East Asian (EAS) AF: 0.368 AC: 1882 AN: 5118

South Asian (SAS) AF: 0.101 AC: 485 AN: 4818

European-Finnish (FIN) AF: 0.0532 AC: 564 AN: 10596

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

European-Non Finnish (NFE) AF: 0.0579 AC: 3925 AN: 67758

Other (OTH) AF: 0.114 AC: 238 AN: 2092

Alfa AF: 0.0723 Hom.: 2258

Bravo AF: 0.0896

Asia WGS AF: 0.199 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.84
DANN	Benign	0.43
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1847461; hg19: chr12-91077508;