Genetic Variant LINC00326:n.210+13679T>C (chr6-132994665-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 ENST00000659399.1(LINC00326):n.210+13679T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 152,038 control chromosomes in the GnomAD database, including 43,032 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 0.74 ( 43032 hom., cov: 32)

Consequence

LINC00326
ENST00000659399.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.55

Publications

17 publications found

Variant links:

COSMIC-nc: COSV71189084

Genes affected

LINC00326 (HGNC:41926): (long intergenic non-protein coding RNA 326)

LINC00326 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC00326	ENST00000659399.1 link	n.210+13679T>C	intron_variant	Intron 2 of 2
LINC00326	ENST00000668229.2 link	n.71+40148T>C	intron_variant	Intron 1 of 2
LINC00326	ENST00000669115.3 link	n.284+40065T>C	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.744

AC:

113094

AN:

151920

Hom.:

42976

Cov.:

show subpopulations

Gnomad AFR

AF:

0.883

Gnomad AMI

AF:

0.588

Gnomad AMR

AF:

0.761

Gnomad ASJ

AF:

0.583

Gnomad EAS

AF:

0.875

Gnomad SAS

AF:

0.799

Gnomad FIN

AF:

0.669

Gnomad MID

AF:

0.623

Gnomad NFE

AF:

0.665

Gnomad OTH

AF:

0.725

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

GnomAD4 genome

AF:

0.745

AC:

113207

AN:

152038

Hom.:

43032

Cov.:

AF XY:

0.747

AC XY:

55507

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.883

AC:

36669

AN:

41506

American (AMR)

AF:

0.761

AC:

11613

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.583

AC:

2024

AN:

3470

East Asian (EAS)

AF:

0.876

AC:

4523

AN:

5164

South Asian (SAS)

AF:

0.800

AC:

3855

AN:

4820

European-Finnish (FIN)

AF:

0.669

AC:

7053

AN:

10546

Middle Eastern (MID)

AF:

0.626

AC:

184

AN:

294

European-Non Finnish (NFE)

AF:

0.665

AC:

45216

AN:

67954

Other (OTH)

AF:

0.726

AC:

1534

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1395

2790

4186

5581

6976

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

842

1684

2526

3368

4210

<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:

0.709

Hom.:

62224

Bravo

AF:

0.756

Asia WGS

AF:

0.831

AC:

2887

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.70

(source)

DANN

Benign

0.64

PhyloP100

-1.5

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