rs1798808

Positions:

• chr12-126700649-G-A

Variant summary

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

The NR_183614.1(LINC02824):​n.363+5059G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 151,984 control chromosomes in the GnomAD database, including 5,516 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 0.24 (5516 hom., cov: 32)
• Consequence: LINC02824 NR_183614.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580

Genes affected

LINC02824 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02824	NR_183614.1	n.363+5059G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02824	ENST00000653842.1	n.379+5059G>A		intron_variant
LINC02824	ENST00000653913.1	n.299+5059G>A		intron_variant
LINC02824	ENST00000667303.1	n.289+8734G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36273 AN: 151864 Hom.: 5499 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.239 AC: 36329 AN: 151984 Hom.: 5516 Cov.: 32 AF XY: 0.236 AC XY: 17536 AN XY: 74284

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.227

Alfa AF: 0.203 Hom.: 476

Bravo AF: 0.251

Asia WGS AF: 0.174 AC: 607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1798808; hg19: chr12-127185195;