Genetic Variant LINC02829:n.319C>T (chr6-29507365-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_183359.1(LINC02829):n.319C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,456 control chromosomes in the GnomAD database, including 1,533 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 0.14 ( 1524 hom., cov: 32)

Exomes 𝑓: 0.18 ( 9 hom. )

Consequence

LINC02829
NR_183359.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.423

Variant links:

Genes affected

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

LINC02829 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02829	NR_183359.1 link	n.319C>T		non_coding_transcript_exon_variant	Exon 3 of 4
LINC02829	NR_183360.1 link	n.387C>T		non_coding_transcript_exon_variant	Exon 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02829	ENST00000436804.2 link	n.319C>T		non_coding_transcript_exon_variant	Exon 3 of 4	5
LINC02829	ENST00000661850.1 link	n.319C>T		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20744

AN:

152032

Hom.:

1519

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0761

Gnomad AMI

AF:

0.176

Gnomad AMR

AF:

0.181

Gnomad ASJ

AF:

0.137

Gnomad EAS

AF:

0.233

Gnomad SAS

AF:

0.154

Gnomad FIN

AF:

0.146

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.152

Gnomad OTH

AF:

0.141

GnomAD4 exome

AF:

0.180

AC:

AN:

306

Hom.:

Cov.:

AF XY:

0.159

AC XY:

AN XY:

232

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.200

Gnomad4 ASJ exome

AF:

0.250

Gnomad4 EAS exome

AF:

0.0833

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.167

Gnomad4 NFE exome

AF:

0.185

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.136

AC:

20751

AN:

152150

Hom.:

1524

Cov.:

AF XY:

0.139

AC XY:

10318

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.0759

Gnomad4 AMR

AF:

0.182

Gnomad4 ASJ

AF:

0.137

Gnomad4 EAS

AF:

0.234

Gnomad4 SAS

AF:

0.154

Gnomad4 FIN

AF:

0.146

Gnomad4 NFE

AF:

0.152

Gnomad4 OTH

AF:

0.141

Alfa

AF:

0.156

Hom.:

2708

Bravo

AF:

0.141

Asia WGS

AF:

0.145

AC:

506

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.8

DANN

Benign

0.59

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over