Genetic Variant LINC01312:n.659T>C (chr6-133837662-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000456347.5(LINC01312):n.659T>C 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 0.277 in 152,194 control chromosomes in the GnomAD database, including 7,092 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 0.28 ( 7067 hom., cov: 30)

Exomes 𝑓: 0.32 ( 25 hom. )

Consequence

LINC01312
ENST00000456347.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.803

Publications

17 publications found

Variant links:

Genes affected

LINC01312 (HGNC:28525): (long intergenic non-protein coding RNA 1312)

LINC01312 links:

TARID (HGNC:50506): (TCF21 antisense RNA inducing promoter demethylation)

TARID 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=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01312	NR_027030.1 link	n.659T>C		non_coding_transcript_exon_variant	Exon 2 of 3
TARID	NR_109982.1 link	n.478+8215A>G		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01312	ENST00000456347.5 link	n.659T>C	non_coding_transcript_exon_variant	Exon 2 of 3	1
TARID	ENST00000607033.5 link	n.454+8215A>G	intron_variant	Intron 2 of 8	1
LINC01312	ENST00000412745.2 link	n.128T>C	non_coding_transcript_exon_variant	Exon 2 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.277

AC:

41969

AN:

151662

Hom.:

7063

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0850

Gnomad AMI

AF:

0.470

Gnomad AMR

AF:

0.244

Gnomad ASJ

AF:

0.318

Gnomad EAS

AF:

0.464

Gnomad SAS

AF:

0.295

Gnomad FIN

AF:

0.277

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.382

Gnomad OTH

AF:

0.256

GnomAD4 exome

AF:

0.321

AC:

133

AN:

414

Hom.:

Cov.:

AF XY:

0.304

AC XY:

AN XY:

240

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.323

AC:

131

AN:

406

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.333

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.520

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.277

AC:

41976

AN:

151780

Hom.:

7067

Cov.:

AF XY:

0.270

AC XY:

20006

AN XY:

74146

show subpopulations

African (AFR)

AF:

0.0849

AC:

3518

AN:

41440

American (AMR)

AF:

0.244

AC:

3719

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.318

AC:

1102

AN:

3464

East Asian (EAS)

AF:

0.464

AC:

2370

AN:

5108

South Asian (SAS)

AF:

0.294

AC:

1411

AN:

4792

European-Finnish (FIN)

AF:

0.277

AC:

2906

AN:

10478

Middle Eastern (MID)

AF:

0.211

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.382

AC:

25921

AN:

67934

Other (OTH)

AF:

0.256

AC:

539

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1394

2789

4183

5578

6972

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

436

872

1308

1744

2180

<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:

0.341

Hom.:

32954

Bravo

AF:

0.266

Asia WGS

AF:

0.335

AC:

1168

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

7.5

(source)

DANN

Benign

0.69

PhyloP100

0.80

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over