dbSNP rs7647526: LINC02053:n.264+14352T>G (chr3-180428809-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000654328.1(LINC02053):n.264+14352T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,190 control chromosomes in the GnomAD database, including 1,847 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 0.10 ( 1847 hom., cov: 32)

Consequence

LINC02053
ENST00000654328.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0590

Publications

1 publications found

Variant links:

Genes affected

LINC02053 (HGNC:52893): (long intergenic non-protein coding RNA 2053)

LINC02053 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02053	ENST00000654328.1 link	n.264+14352T>G	intron_variant	Intron 1 of 1
LINC02053	ENST00000668671.2 link	n.282+14352T>G	intron_variant	Intron 1 of 1
LINC02053	ENST00000831001.1 link	n.294+14352T>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15647

AN:

152072

Hom.:

1839

Cov.:

show subpopulations

Gnomad AFR

AF:

0.291

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0521

Gnomad ASJ

AF:

0.0297

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.00620

Gnomad FIN

AF:

0.00744

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.0352

Gnomad OTH

AF:

0.0822

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

GnomAD4 genome

AF:

0.103

AC:

15688

AN:

152190

Hom.:

1847

Cov.:

AF XY:

0.0995

AC XY:

7407

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.291

AC:

12079

AN:

41468

American (AMR)

AF:

0.0518

AC:

793

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0297

AC:

103

AN:

3470

East Asian (EAS)

AF:

0.000771

AC:

AN:

5186

South Asian (SAS)

AF:

0.00600

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.00744

AC:

AN:

10614

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0352

AC:

2392

AN:

68004

Other (OTH)

AF:

0.0833

AC:

176

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

614

1228

1843

2457

3071

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

152

304

456

608

760

<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:

0.0470

Hom.:

326

Bravo

AF:

0.115

Asia WGS

AF:

0.0220

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.7

(source)

DANN

Benign

0.56

PhyloP100

0.059

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