Genetic Variant LINC01579:n.489-5025A>G (chr15-93766152-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 ENST00000553818.1(LINC01579):n.489-5025A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,222 control chromosomes in the GnomAD database, including 1,586 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 ( 1586 hom., cov: 32)

Consequence

LINC01579
ENST00000553818.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.562

Publications

1 publications found

Variant links:

Genes affected

LINC01579 (HGNC:27519): (long intergenic non-protein coding RNA 1579)

LINC01579 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 = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01579	ENST00000553818.1 link	n.489-5025A>G		intron_variant	Intron 3 of 3	4
LINC01579	ENST00000557481.6 link	n.541-5025A>G		intron_variant	Intron 4 of 6	5

Frequencies

GnomAD3 genomes

AF:

0.140

AC:

21341

AN:

152104

Hom.:

1588

Cov.:

show subpopulations

Gnomad AFR

AF:

0.136

Gnomad AMI

AF:

0.116

Gnomad AMR

AF:

0.174

Gnomad ASJ

AF:

0.147

Gnomad EAS

AF:

0.254

Gnomad SAS

AF:

0.0876

Gnomad FIN

AF:

0.148

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.129

Gnomad OTH

AF:

0.154

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

GnomAD4 genome

AF:

0.140

AC:

21353

AN:

152222

Hom.:

1586

Cov.:

AF XY:

0.140

AC XY:

10421

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.135

AC:

5626

AN:

41534

American (AMR)

AF:

0.174

AC:

2660

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.147

AC:

509

AN:

3472

East Asian (EAS)

AF:

0.254

AC:

1312

AN:

5160

South Asian (SAS)

AF:

0.0870

AC:

420

AN:

4826

European-Finnish (FIN)

AF:

0.148

AC:

1570

AN:

10598

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.129

AC:

8781

AN:

68014

Other (OTH)

AF:

0.155

AC:

328

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

941

1882

2822

3763

4704

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

230

460

690

920

1150

<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:

0.136

Hom.:

1100

Bravo

AF:

0.146

Asia WGS

AF:

0.156

AC:

541

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

1.0

(source)

DANN

Benign

0.53

PhyloP100

-0.56

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