Genetic Variant LINC02742:n.304+124311T>C (chr11-28866219-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 ENST00000513853.6(LINC02742):n.304+124311T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,036 control chromosomes in the GnomAD database, including 10,517 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 0.36 ( 10517 hom., cov: 32)

Consequence

LINC02742
ENST00000513853.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.780

Publications

1 publications found

Variant links:

Genes affected

LINC02742 (HGNC:54259): (long intergenic non-protein coding RNA 2742)

LINC02742 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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02742	ENST00000513853.6 link	n.304+124311T>C	intron_variant	Intron 2 of 3	3
LINC02742	ENST00000662190.1 link	n.313-16970T>C	intron_variant	Intron 2 of 2
LINC02742	ENST00000788052.1 link	n.295-50662T>C	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.361

AC:

54795

AN:

151918

Hom.:

10504

Cov.:

show subpopulations

Gnomad AFR

AF:

0.247

Gnomad AMI

AF:

0.553

Gnomad AMR

AF:

0.410

Gnomad ASJ

AF:

0.402

Gnomad EAS

AF:

0.340

Gnomad SAS

AF:

0.277

Gnomad FIN

AF:

0.302

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.430

Gnomad OTH

AF:

0.403

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

GnomAD4 genome

AF:

0.361

AC:

54850

AN:

152036

Hom.:

10517

Cov.:

AF XY:

0.353

AC XY:

26263

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.247

AC:

10258

AN:

41480

American (AMR)

AF:

0.410

AC:

6256

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.402

AC:

1394

AN:

3470

East Asian (EAS)

AF:

0.340

AC:

1748

AN:

5146

South Asian (SAS)

AF:

0.276

AC:

1330

AN:

4820

European-Finnish (FIN)

AF:

0.302

AC:

3193

AN:

10574

Middle Eastern (MID)

AF:

0.354

AC:

104

AN:

294

European-Non Finnish (NFE)

AF:

0.430

AC:

29204

AN:

67980

Other (OTH)

AF:

0.408

AC:

861

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1727

3454

5181

6908

8635

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

536

1072

1608

2144

2680

<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:

0.415

Hom.:

56951

Bravo

AF:

0.370

Asia WGS

AF:

0.350

AC:

1220

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.87

(source)

DANN

Benign

0.79

PhyloP100

-0.78

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