ENST00000652014.1:n.860+51194G>A

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 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+51194G>A		intron_variant	Intron 5 of 5
LINC02822	ENST00000664727.1	n.121+54527G>A		intron_variant	Intron 2 of 5
LINC02822	ENST00000666236.1	n.198+54488G>A		intron_variant	Intron 2 of 4
ENSG00000288102	ENST00000670607.1	n.288+9924C>T		intron_variant	Intron 3 of 7

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

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.0997

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.0157

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.131

Alfa AF: 0.147 Hom.: 3416

Bravo AF: 0.143

Asia WGS AF: 0.0970 AC: 339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1948839; hg19: chr12-91124916;