rs1948839

Variant names:

• chr12-90731139-G-A
• rs1948839
• ENST00000652014.1:n.860+51194G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000652014.1(LINC02822):​n.860+51194G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,058 control chromosomes in the GnomAD database, including 1,704 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 0.15 (1704 hom., cov: 32)
• Consequence: LINC02822 ENST00000652014.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 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+51194G>A		intron	N/A
	LINC02822	ENST00000664727.1		n.121+54527G>A		intron	N/A
	LINC02822	ENST00000666236.1		n.198+54488G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22057 AN: 151940 Hom.: 1702 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0999

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0158

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.145 AC: 22087 AN: 152058 Hom.: 1704 Cov.: 32 AF XY: 0.142 AC XY: 10559 AN XY: 74320

African (AFR) AF: 0.178 AC: 7374 AN: 41474

American (AMR) AF: 0.0997 AC: 1523 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3464

East Asian (EAS) AF: 0.0157 AC: 81 AN: 5172

South Asian (SAS) AF: 0.119 AC: 573 AN: 4830

European-Finnish (FIN) AF: 0.142 AC: 1503 AN: 10574

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10276 AN: 67956

Other (OTH) AF: 0.131 AC: 276 AN: 2112

Alfa AF: 0.148 Hom.: 5467

Bravo AF: 0.143

Asia WGS AF: 0.0970 AC: 339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.3
DANN	Benign	0.64
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs1948839; hg19: chr12-91124916;