6-29501875-G-A

Variant names:

• chr6-29501875-G-A
• rs1233486
• ENST00000436804.3:n.68-3446G>A

Variant summary

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

The ENST00000436804.3(LINC02829):​n.68-3446G>A variant causes a intron 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 ENST00000436804.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.486
• Publications: 15 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000436804.3. 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
	LINC02829	NR_183359.1		n.66-3446G>A		intron	N/A
	LINC02829	NR_183360.1		n.134-3446G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02829	ENST00000436804.3	TSL:5	n.68-3446G>A		intron	N/A
	LINC02829	ENST00000661850.2		n.197-3446G>A		intron	N/A
	LINC02829	ENST00000824900.1		n.136-3446G>A		intron	N/A

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

African (AFR) AF: 0.0809 AC: 3357 AN: 41502

American (AMR) AF: 0.178 AC: 2725 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3470

East Asian (EAS) AF: 0.174 AC: 898 AN: 5168

South Asian (SAS) AF: 0.326 AC: 1567 AN: 4810

European-Finnish (FIN) AF: 0.412 AC: 4338 AN: 10532

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18217 AN: 67984

Other (OTH) AF: 0.208 AC: 439 AN: 2112

Alfa AF: 0.243 Hom.: 16216

Bravo AF: 0.185

Asia WGS AF: 0.309 AC: 1074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.51
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs1233486; hg19: chr6-29469652;