Genetic Variant ENST00000660637.1:n.156+5809C>T (chr6-82095836-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 ENST00000660637.1(LINC02542):n.156+5809C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,178 control chromosomes in the GnomAD database, including 897 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 ( 897 hom., cov: 32)

Consequence

LINC02542
ENST00000660637.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0330

Publications

3 publications found

Variant links:

Genes affected

LINC02542 (HGNC:53576): (long intergenic non-protein coding RNA 2542)

LINC02542 links:

ENSG00000306836 (HGNC:):

ENSG00000306836 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=-0.92).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02542	NR_149135.1 link	n.206+5724C>T		intron_variant	Intron 1 of 3
LOC107986617	XR_001744231.2 link	n.751-17621G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02542	ENST00000660637.1 link	n.156+5809C>T	intron_variant	Intron 1 of 2
LINC02542	ENST00000663543.1 link	n.290-37831C>T	intron_variant	Intron 2 of 3
LINC02542	ENST00000666226.1 link	n.121+5809C>T	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

15913

AN:

152060

Hom.:

895

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0813

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.157

Gnomad ASJ

AF:

0.0877

Gnomad EAS

AF:

0.115

Gnomad SAS

AF:

0.155

Gnomad FIN

AF:

0.0818

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.107

Gnomad OTH

AF:

0.108

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

GnomAD4 genome

AF:

0.105

AC:

15944

AN:

152178

Hom.:

897

Cov.:

AF XY:

0.106

AC XY:

7878

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.0816

AC:

3389

AN:

41536

American (AMR)

AF:

0.157

AC:

2405

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0877

AC:

304

AN:

3468

East Asian (EAS)

AF:

0.116

AC:

599

AN:

5170

South Asian (SAS)

AF:

0.156

AC:

752

AN:

4820

European-Finnish (FIN)

AF:

0.0818

AC:

867

AN:

10600

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.107

AC:

7252

AN:

67990

Other (OTH)

AF:

0.108

AC:

227

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

731

1462

2193

2924

3655

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

186

372

558

744

930

<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:

0.109

Hom.:

746

Bravo

AF:

0.109

Asia WGS

AF:

0.149

AC:

519

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.7

(source)

DANN

Benign

0.28

PhyloP100

0.033

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