dbSNP rs2651432: LINC02249:n.601-149T>C (chr15-30323066-T-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000749194.1(LINC02249):n.601-149T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.35 ( 242 hom., cov: 29)

Failed GnomAD Quality Control

Consequence

LINC02249
ENST00000749194.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.330

Publications

1 publications found

Variant links:

Genes affected

LINC02249 (HGNC:32351): (long intergenic non-protein coding RNA 2249)

LINC02249 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02249	ENST00000749194.1 link	n.601-149T>C	intron_variant	Intron 3 of 8
LINC02249	ENST00000749195.1 link	n.464-149T>C	intron_variant	Intron 3 of 9
LINC02249	ENST00000749196.1 link	n.429-149T>C	intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes

AF:

0.354

AC:

48790

AN:

137832

Hom.:

241

Cov.:

show subpopulations

Gnomad AFR

AF:

0.282

Gnomad AMI

AF:

0.360

Gnomad AMR

AF:

0.326

Gnomad ASJ

AF:

0.408

Gnomad EAS

AF:

0.386

Gnomad SAS

AF:

0.424

Gnomad FIN

AF:

0.400

Gnomad MID

AF:

0.396

Gnomad NFE

AF:

0.385

Gnomad OTH

AF:

0.359

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

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff

AF:

0.354

AC:

48822

AN:

137940

Hom.:

242

Cov.:

AF XY:

0.355

AC XY:

23895

AN XY:

67336

show subpopulations

African (AFR)

AF:

0.282

AC:

10448

AN:

37026

American (AMR)

AF:

0.325

AC:

4470

AN:

13740

Ashkenazi Jewish (ASJ)

AF:

0.408

AC:

1312

AN:

3212

East Asian (EAS)

AF:

0.387

AC:

1751

AN:

4530

South Asian (SAS)

AF:

0.424

AC:

1838

AN:

4336

European-Finnish (FIN)

AF:

0.400

AC:

3892

AN:

9738

Middle Eastern (MID)

AF:

0.393

AC:

103

AN:

262

European-Non Finnish (NFE)

AF:

0.385

AC:

24037

AN:

62396

Other (OTH)

AF:

0.360

AC:

671

AN:

1866

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.407

Heterozygous variant carriers

1595

3190

4784

6379

7974

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

598

1196

1794

2392

2990

<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:

0.366

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

(source)

DANN

Benign

0.85

PhyloP100

0.33

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