dbSNP rs16893523: LINC01526:n.85-1437C>T (chr6-81794462-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000848188.1(LINC01526):n.85-1437C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 151,724 control chromosomes in the GnomAD database, including 939 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 0.10 ( 939 hom., cov: 32)

Consequence

LINC01526
ENST00000848188.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.765

Publications

3 publications found

Variant links:

Genes affected

LINC01526 (HGNC:51265): (long intergenic non-protein coding RNA 1526)

LINC01526 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=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC01526	ENST00000848188.1 link	n.85-1437C>T	intron_variant	Intron 1 of 1
LINC01526	ENST00000848189.1 link	n.194-1437C>T	intron_variant	Intron 2 of 2
LINC01526	ENST00000848190.1 link	n.668-1437C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15797

AN:

151608

Hom.:

935

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.0760

Gnomad AMR

AF:

0.146

Gnomad ASJ

AF:

0.139

Gnomad EAS

AF:

0.189

Gnomad SAS

AF:

0.119

Gnomad FIN

AF:

0.0251

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.0871

Gnomad OTH

AF:

0.120

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

GnomAD4 genome

AF:

0.104

AC:

15816

AN:

151724

Hom.:

939

Cov.:

AF XY:

0.104

AC XY:

7687

AN XY:

74136

show subpopulations

African (AFR)

AF:

0.122

AC:

5047

AN:

41440

American (AMR)

AF:

0.146

AC:

2217

AN:

15194

Ashkenazi Jewish (ASJ)

AF:

0.139

AC:

480

AN:

3464

East Asian (EAS)

AF:

0.190

AC:

971

AN:

5122

South Asian (SAS)

AF:

0.120

AC:

577

AN:

4818

European-Finnish (FIN)

AF:

0.0251

AC:

265

AN:

10566

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0871

AC:

5906

AN:

67810

Other (OTH)

AF:

0.119

AC:

250

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

716

1432

2149

2865

3581

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

168

336

504

672

840

<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:

0.103

Hom.:

146

Bravo

AF:

0.117

Asia WGS

AF:

0.140

AC:

490

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.58

(source)

DANN

Benign

0.61

PhyloP100

-0.77

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