Genetic Variant LINC02829:n.321C>T (chr6-29507365-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000436804.3(LINC02829):n.321C>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
ENST00000436804.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.423

Publications

13 publications found

Variant links:

Genes affected

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

LINC02829 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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	Effect	Exon rank	TSL
LINC02829	ENST00000436804.3 link	n.321C>T	non_coding_transcript_exon_variant	Exon 3 of 4	5
LINC02829	ENST00000661850.2 link	n.450C>T	non_coding_transcript_exon_variant	Exon 3 of 3
LINC02829	ENST00000824900.1 link	n.389C>T	non_coding_transcript_exon_variant	Exon 4 of 5

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

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.200

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AF:

0.0833

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.167

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.185

AC:

AN:

238

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.136

AC:

20751

AN:

152150

Hom.:

1524

Cov.:

AF XY:

0.139

AC XY:

10318

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.0759

AC:

3150

AN:

41518

American (AMR)

AF:

0.182

AC:

2779

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.137

AC:

476

AN:

3472

East Asian (EAS)

AF:

0.234

AC:

1209

AN:

5170

South Asian (SAS)

AF:

0.154

AC:

742

AN:

4816

European-Finnish (FIN)

AF:

0.146

AC:

1547

AN:

10582

Middle Eastern (MID)

AF:

0.129

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.152

AC:

10352

AN:

67968

Other (OTH)

AF:

0.141

AC:

298

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

950

1900

2851

3801

4751

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

240

480

720

960

1200

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.149

Hom.:

4571

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

(source)

DANN

Benign

0.59

PhyloP100

0.42

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over