dbSNP rs12606608: LINC01539:n.530G>A (chr18-56188320-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 ENST00000382897.2(LINC01539):n.530G>A 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 0.522 in 151,980 control chromosomes in the GnomAD database, including 21,731 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 0.52 ( 21727 hom., cov: 31)

Exomes 𝑓: 0.50 ( 4 hom. )

Consequence

LINC01539
ENST00000382897.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.852

Publications

4 publications found

Variant links:

Genes affected

LINC01539 (HGNC:51307): (long intergenic non-protein coding RNA 1539)

LINC01539 links:

LINC03069 (HGNC:56641): (long intergenic non-protein coding RNA 3069)

LINC03069 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000382897.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000382897.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03069	NR_148972.1		n.530G>A		non_coding_transcript_exon	Exon 2 of 9

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
LINC01539	ENST00000382897.2	TSL:2	n.530G>A	non_coding_transcript_exon	Exon 2 of 9
LINC01539	ENST00000715823.1		n.215G>A	non_coding_transcript_exon	Exon 1 of 4
LINC01539	ENST00000765111.1		n.186G>A	non_coding_transcript_exon	Exon 2 of 5

Frequencies

GnomAD3 genomes

AF:

0.522

AC:

79219

AN:

151840

Hom.:

21718

Cov.:

show subpopulations

Gnomad AFR

AF:

0.343

Gnomad AMI

AF:

0.416

Gnomad AMR

AF:

0.569

Gnomad ASJ

AF:

0.598

Gnomad EAS

AF:

0.840

Gnomad SAS

AF:

0.552

Gnomad FIN

AF:

0.597

Gnomad MID

AF:

0.535

Gnomad NFE

AF:

0.578

Gnomad OTH

AF:

0.558

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.438

AC XY:

AN XY:

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

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)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.556

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.00000907115), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.325

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.522

AC:

79256

AN:

151958

Hom.:

21727

Cov.:

AF XY:

0.527

AC XY:

39120

AN XY:

74256

show subpopulations

African (AFR)

AF:

0.343

AC:

14208

AN:

41424

American (AMR)

AF:

0.568

AC:

8676

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.598

AC:

2072

AN:

3466

East Asian (EAS)

AF:

0.839

AC:

4322

AN:

5152

South Asian (SAS)

AF:

0.551

AC:

2659

AN:

4824

European-Finnish (FIN)

AF:

0.597

AC:

6296

AN:

10552

Middle Eastern (MID)

AF:

0.541

AC:

159

AN:

294

European-Non Finnish (NFE)

AF:

0.578

AC:

39304

AN:

67960

Other (OTH)

AF:

0.561

AC:

1183

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1865

3729

5594

7458

9323

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

694

1388

2082

2776

3470

<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:

0.565

Hom.:

31005

Bravo

AF:

0.512

Asia WGS

AF:

0.649

AC:

2256

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.1

(source)

DANN

Benign

0.69

PhyloP100

-0.85

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over