rs1233486

Positions:

• chr6-29501875-G-A

Variant summary

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

The NR_183360.1(LINC02829):​n.134-3446G>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 0.213 in 152,076 control chromosomes in the GnomAD database, including 4,180 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 0.21 (4180 hom., cov: 32)
• Consequence: LINC02829 NR_183360.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.486

Genes affected

LINC02829 (HGNC:54362): (long intergenic non-protein coding RNA 2829)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02829	NR_183360.1	n.134-3446G>A		intron_variant, non_coding_transcript_variant
LINC02829	NR_183359.1	n.66-3446G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02829	ENST00000436804.2	n.66-3446G>A		intron_variant, non_coding_transcript_variant		5
LINC02829	ENST00000661850.1	n.66-3446G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32311 AN: 151956 Hom.: 4166 Cov.: 32

Gnomad AFR AF: 0.0809

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.213 AC: 32329 AN: 152076 Hom.: 4180 Cov.: 32 AF XY: 0.219 AC XY: 16292 AN XY: 74312

Gnomad4 AFR AF: 0.0809

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.208

Alfa AF: 0.253 Hom.: 6713

Bravo AF: 0.185

Asia WGS AF: 0.309 AC: 1074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1233486; hg19: chr6-29469652;