Genetic Variant LINC02526:n.266+1106T>G (chr6-106697506-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000424162.2(LINC02526):n.266+1106T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0345 in 152,326 control chromosomes in the GnomAD database, including 289 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 0.034 ( 289 hom., cov: 33)

Consequence

LINC02526
ENST00000424162.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.640

Publications

2 publications found

Variant links:

Genes affected

LINC02526 (HGNC:53550): (long intergenic non-protein coding RNA 2526)

LINC02526 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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02526	NR_149100.1 link	n.316+1106T>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02526	ENST00000424162.2 link	n.266+1106T>G		intron_variant	Intron 2 of 2	2
LINC02526	ENST00000771592.1 link	n.632+1106T>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0344

AC:

5239

AN:

152208

Hom.:

285

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00492

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.112

Gnomad ASJ

AF:

0.00490

Gnomad EAS

AF:

0.210

Gnomad SAS

AF:

0.0281

Gnomad FIN

AF:

0.104

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0130

Gnomad OTH

AF:

0.0377

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

GnomAD4 genome

AF:

0.0345

AC:

5248

AN:

152326

Hom.:

289

Cov.:

AF XY:

0.0400

AC XY:

2983

AN XY:

74496

show subpopulations

African (AFR)

AF:

0.00491

AC:

204

AN:

41580

American (AMR)

AF:

0.113

AC:

1729

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.00490

AC:

AN:

3472

East Asian (EAS)

AF:

0.211

AC:

1091

AN:

5182

South Asian (SAS)

AF:

0.0278

AC:

134

AN:

4828

European-Finnish (FIN)

AF:

0.104

AC:

1108

AN:

10614

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0130

AC:

887

AN:

68032

Other (OTH)

AF:

0.0369

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

244

487

731

974

1218

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

174

232

290

<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:

0.0276

Hom.:

Bravo

AF:

0.0366

Asia WGS

AF:

0.0980

AC:

338

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.6

(source)

DANN

Benign

0.73

PhyloP100

-0.64

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