Genetic Variant LINC01324:n.76+20807A>G (chr3-164882802-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 ENST00000497379.3(LINC01324):n.76+20807A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 151,906 control chromosomes in the GnomAD database, including 7,743 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 ( 7743 hom., cov: 32)

Consequence

LINC01324
ENST00000497379.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.167

Publications

7 publications found

Variant links:

Genes affected

LINC01324 (HGNC:50530): (long intergenic non-protein coding RNA 1324)

LINC01324 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 (EAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01324	ENST00000497379.3 link	n.76+20807A>G	intron_variant	Intron 1 of 4	5
LINC01324	ENST00000715736.1 link	n.209+15621A>G	intron_variant	Intron 3 of 7
LINC01324	ENST00000722128.1 link	n.539+15621A>G	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.280

AC:

42482

AN:

151788

Hom.:

7728

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0675

Gnomad AMI

AF:

0.482

Gnomad AMR

AF:

0.415

Gnomad ASJ

AF:

0.326

Gnomad EAS

AF:

0.677

Gnomad SAS

AF:

0.358

Gnomad FIN

AF:

0.368

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.325

Gnomad OTH

AF:

0.292

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

GnomAD4 genome

AF:

0.280

AC:

42502

AN:

151906

Hom.:

7743

Cov.:

AF XY:

0.287

AC XY:

21330

AN XY:

74196

show subpopulations

African (AFR)

AF:

0.0673

AC:

2797

AN:

41548

American (AMR)

AF:

0.415

AC:

6332

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.326

AC:

1130

AN:

3462

East Asian (EAS)

AF:

0.677

AC:

3463

AN:

5112

South Asian (SAS)

AF:

0.359

AC:

1727

AN:

4816

European-Finnish (FIN)

AF:

0.368

AC:

3880

AN:

10534

Middle Eastern (MID)

AF:

0.276

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.325

AC:

22024

AN:

67862

Other (OTH)

AF:

0.298

AC:

630

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1383

2766

4148

5531

6914

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

428

856

1284

1712

2140

<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:

0.304

Hom.:

16283

Bravo

AF:

0.277

Asia WGS

AF:

0.488

AC:

1693

AN:

3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

6.8

(source)

DANN

Benign

0.59

PhyloP100

0.17

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