Genetic Variant LINC02743:n.379-7913G>A (chr11-133661760-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 ENST00000762255.1(LINC02743):n.379-7913G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0442 in 152,230 control chromosomes in the GnomAD database, including 480 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 0.044 ( 480 hom., cov: 32)

Consequence

LINC02743
ENST00000762255.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0760

Publications

2 publications found

Variant links:

Genes affected

LINC02743 (HGNC:54261): (long intergenic non-protein coding RNA 2743)

LINC02743 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=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02743	ENST00000762255.1 link	n.379-7913G>A	intron_variant	Intron 3 of 6
LINC02743	ENST00000762256.1 link	n.389-7913G>A	intron_variant	Intron 3 of 4
LINC02743	ENST00000762257.1 link	n.403-7913G>A	intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes

AF:

0.0441

AC:

6714

AN:

152112

Hom.:

481

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0696

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0954

Gnomad ASJ

AF:

0.0112

Gnomad EAS

AF:

0.309

Gnomad SAS

AF:

0.0488

Gnomad FIN

AF:

0.00613

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00516

Gnomad OTH

AF:

0.0397

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

GnomAD4 genome

AF:

0.0442

AC:

6722

AN:

152230

Hom.:

480

Cov.:

AF XY:

0.0465

AC XY:

3461

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.0696

AC:

2890

AN:

41530

American (AMR)

AF:

0.0956

AC:

1462

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0112

AC:

AN:

3472

East Asian (EAS)

AF:

0.309

AC:

1597

AN:

5164

South Asian (SAS)

AF:

0.0484

AC:

233

AN:

4816

European-Finnish (FIN)

AF:

0.00613

AC:

AN:

10608

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00516

AC:

351

AN:

68026

Other (OTH)

AF:

0.0393

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

308

615

923

1230

1538

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

216

288

360

<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:

0.0285

Hom.:

330

Bravo

AF:

0.0538

Asia WGS

AF:

0.141

AC:

489

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.35

(source)

DANN

Benign

0.42

PhyloP100

-0.076

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