dbSNP rs6801136: LINC02030:n.202+440C>T (chr3-55231293-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 ENST00000654581.1(LINC02030):n.202+440C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,998 control chromosomes in the GnomAD database, including 7,846 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 0.32 ( 7846 hom., cov: 32)

Consequence

LINC02030
ENST00000654581.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.460

Publications

2 publications found

Variant links:

Genes affected

LINC02030 (HGNC:52864): (long intergenic non-protein coding RNA 2030)

LINC02030 links:

LOC124906243 (HGNC:):

LOC124906243 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=-1.03).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02030	NR_183740.1 link	n.352+436C>T	intron_variant	Intron 3 of 6
LINC02030	NR_183741.1 link	n.209+440C>T	intron_variant	Intron 2 of 8
LINC02030	NR_183742.1 link	n.114+4325C>T	intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02030	ENST00000654581.1 link	n.202+440C>T	intron_variant	Intron 2 of 5
LINC02030	ENST00000662390.1 link	n.160+436C>T	intron_variant	Intron 2 of 5
LINC02030	ENST00000809726.1 link	n.284+41679C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.318

AC:

48309

AN:

151880

Hom.:

7835

Cov.:

show subpopulations

Gnomad AFR

AF:

0.296

Gnomad AMI

AF:

0.229

Gnomad AMR

AF:

0.366

Gnomad ASJ

AF:

0.334

Gnomad EAS

AF:

0.176

Gnomad SAS

AF:

0.179

Gnomad FIN

AF:

0.325

Gnomad MID

AF:

0.296

Gnomad NFE

AF:

0.340

Gnomad OTH

AF:

0.321

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

GnomAD4 genome

AF:

0.318

AC:

48353

AN:

151998

Hom.:

7846

Cov.:

AF XY:

0.315

AC XY:

23384

AN XY:

74266

show subpopulations

African (AFR)

AF:

0.296

AC:

12278

AN:

41452

American (AMR)

AF:

0.366

AC:

5592

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.334

AC:

1160

AN:

3468

East Asian (EAS)

AF:

0.176

AC:

911

AN:

5164

South Asian (SAS)

AF:

0.179

AC:

865

AN:

4822

European-Finnish (FIN)

AF:

0.325

AC:

3430

AN:

10562

Middle Eastern (MID)

AF:

0.308

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.340

AC:

23134

AN:

67946

Other (OTH)

AF:

0.324

AC:

685

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1656

3313

4969

6626

8282

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

480

960

1440

1920

2400

<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:

0.331

Hom.:

16359

Bravo

AF:

0.321

Asia WGS

AF:

0.198

AC:

687

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.79

(source)

DANN

Benign

0.46

PhyloP100

-0.46

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