dbSNP rs2836823: LINC02940:n.243-92G>A (chr21-39008323-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 ENST00000419664.1(LINC02940):n.243-92G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,180 control chromosomes in the GnomAD database, including 9,337 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 0.31 ( 9334 hom., cov: 32)

Exomes 𝑓: 0.46 ( 3 hom. )

Consequence

LINC02940
ENST00000419664.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.727

Publications

21 publications found

Variant links:

Genes affected

LINC02940 (HGNC:55955): (long intergenic non-protein coding RNA 2940)

LINC02940 links:

ENSG00000296867 (HGNC:):

ENSG00000296867 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 (NFE) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02940	XR_007067865.1 link	n.6954-1539G>A	intron_variant	Intron 2 of 4
LINC02940	XR_007067866.1 link	n.6954-1539G>A	intron_variant	Intron 2 of 3
LINC02940	XR_007067867.1 link	n.6954-1539G>A	intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02940	ENST00000419664.1 link	n.243-92G>A	intron_variant	Intron 1 of 2	5
LINC02940	ENST00000652155.1 link	n.1432-1539G>A	intron_variant	Intron 3 of 4
ENSG00000296867	ENST00000743249.1 link	n.114-517C>T	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.309

AC:

46976

AN:

152034

Hom.:

9337

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0844

Gnomad AMI

AF:

0.365

Gnomad AMR

AF:

0.352

Gnomad ASJ

AF:

0.318

Gnomad EAS

AF:

0.0433

Gnomad SAS

AF:

0.194

Gnomad FIN

AF:

0.404

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.449

Gnomad OTH

AF:

0.293

GnomAD4 exome

AF:

0.464

AC:

AN:

Hom.:

AF XY:

0.400

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.591

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.309

AC:

46982

AN:

152152

Hom.:

9334

Cov.:

AF XY:

0.304

AC XY:

22618

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.0842

AC:

3499

AN:

41534

American (AMR)

AF:

0.352

AC:

5379

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.318

AC:

1102

AN:

3468

East Asian (EAS)

AF:

0.0436

AC:

226

AN:

5180

South Asian (SAS)

AF:

0.195

AC:

940

AN:

4828

European-Finnish (FIN)

AF:

0.404

AC:

4266

AN:

10562

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.449

AC:

30535

AN:

67984

Other (OTH)

AF:

0.294

AC:

621

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1483

2966

4450

5933

7416

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

450

900

1350

1800

2250

<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:

0.399

Hom.:

55048

Bravo

AF:

0.299

Asia WGS

AF:

0.125

AC:

439

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

0.70

(source)

DANN

Benign

0.20

PhyloP100

-0.73

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over