dbSNP rs10894727: LINC02743:n.378+30627A>G (chr11-133694740-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 ENST00000762255.1(LINC02743):n.378+30627A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 152,052 control chromosomes in the GnomAD database, including 24,616 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 0.56 ( 24616 hom., cov: 32)

Consequence

LINC02743
ENST00000762255.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.64

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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 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.378+30627A>G	intron_variant	Intron 3 of 6
LINC02743	ENST00000762256.1 link	n.388+30627A>G	intron_variant	Intron 3 of 4
LINC02743	ENST00000762257.1 link	n.402+30627A>G	intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes

AF:

0.555

AC:

84364

AN:

151934

Hom.:

24601

Cov.:

show subpopulations

Gnomad AFR

AF:

0.423

Gnomad AMI

AF:

0.521

Gnomad AMR

AF:

0.648

Gnomad ASJ

AF:

0.559

Gnomad EAS

AF:

0.902

Gnomad SAS

AF:

0.867

Gnomad FIN

AF:

0.660

Gnomad MID

AF:

0.576

Gnomad NFE

AF:

0.551

Gnomad OTH

AF:

0.532

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

GnomAD4 genome

AF:

0.555

AC:

84410

AN:

152052

Hom.:

24616

Cov.:

AF XY:

0.570

AC XY:

42386

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.423

AC:

17542

AN:

41458

American (AMR)

AF:

0.649

AC:

9922

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.559

AC:

1940

AN:

3472

East Asian (EAS)

AF:

0.901

AC:

4654

AN:

5164

South Asian (SAS)

AF:

0.868

AC:

4175

AN:

4810

European-Finnish (FIN)

AF:

0.660

AC:

6980

AN:

10580

Middle Eastern (MID)

AF:

0.568

AC:

166

AN:

292

European-Non Finnish (NFE)

AF:

0.551

AC:

37423

AN:

67962

Other (OTH)

AF:

0.537

AC:

1133

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1843

3687

5530

7374

9217

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

730

1460

2190

2920

3650

<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:

0.549

Hom.:

29325

Bravo

AF:

0.545

Asia WGS

AF:

0.852

AC:

2962

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

6.7

(source)

DANN

Benign

0.59

PhyloP100

1.6

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