rs1948839

chr12-90731139-G-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, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

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=-0.9).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02822	ENST00000652014.1	n.860+51194G>A		intron_variant, non_coding_transcript_variant
	ENST00000670607.1	n.288+9924C>T		intron_variant, non_coding_transcript_variant
LINC02822	ENST00000664727.1	n.121+54527G>A		intron_variant, non_coding_transcript_variant
LINC02822	ENST00000666236.1	n.198+54488G>A		intron_variant, non_coding_transcript_variant

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;