dbSNP rs4521323: LINC02269:n.56-607A>C (chr4-173734763-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000654333.1(LINC02269):n.56-607A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,714 control chromosomes in the GnomAD database, including 20,669 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 0.51 ( 20669 hom., cov: 30)

Consequence

LINC02269
ENST00000654333.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.818

Publications

6 publications found

Variant links:

Genes affected

LINC02269 (HGNC:53184): (long intergenic non-protein coding RNA 2269)

LINC02269 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02269	ENST00000654333.1 link	n.56-607A>C	intron_variant	Intron 1 of 6
LINC02269	ENST00000654653.1 link	n.56-607A>C	intron_variant	Intron 1 of 3
LINC02269	ENST00000654916.1 link	n.56-607A>C	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.511

AC:

77433

AN:

151598

Hom.:

20658

Cov.:

show subpopulations

Gnomad AFR

AF:

0.356

Gnomad AMI

AF:

0.508

Gnomad AMR

AF:

0.649

Gnomad ASJ

AF:

0.602

Gnomad EAS

AF:

0.768

Gnomad SAS

AF:

0.556

Gnomad FIN

AF:

0.485

Gnomad MID

AF:

0.544

Gnomad NFE

AF:

0.550

Gnomad OTH

AF:

0.532

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

GnomAD4 genome

AF:

0.511

AC:

77467

AN:

151714

Hom.:

20669

Cov.:

AF XY:

0.513

AC XY:

38053

AN XY:

74114

show subpopulations

African (AFR)

AF:

0.356

AC:

14698

AN:

41334

American (AMR)

AF:

0.649

AC:

9878

AN:

15212

Ashkenazi Jewish (ASJ)

AF:

0.602

AC:

2088

AN:

3468

East Asian (EAS)

AF:

0.767

AC:

3909

AN:

5094

South Asian (SAS)

AF:

0.554

AC:

2666

AN:

4808

European-Finnish (FIN)

AF:

0.485

AC:

5105

AN:

10534

Middle Eastern (MID)

AF:

0.544

AC:

160

AN:

294

European-Non Finnish (NFE)

AF:

0.550

AC:

37372

AN:

67956

Other (OTH)

AF:

0.537

AC:

1129

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

1859

3717

5576

7434

9293

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

696

1392

2088

2784

3480

<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:

0.546

Hom.:

94901

Bravo

AF:

0.517

Asia WGS

AF:

0.641

AC:

2231

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

3.0

(source)

DANN

Benign

0.48

PhyloP100

0.82

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