dbSNP rs12146602: LINC02545:n.79-5899C>T (chr11-13833179-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000530492.1(LINC02545):n.79-5899C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,116 control chromosomes in the GnomAD database, including 1,597 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 0.12 ( 1597 hom., cov: 32)

Consequence

LINC02545
ENST00000530492.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.281

Publications

2 publications found

Variant links:

Genes affected

LINC02545 (HGNC:53580): (long intergenic non-protein coding RNA 2545)

LINC02545 links:

LINC02548 (HGNC:53583): (long intergenic non-protein coding RNA 2548)

LINC02548 links:

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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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02548	NR_149108.1 link	n.201-14528G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02545	ENST00000530492.1 link	n.79-5899C>T	intron_variant	Intron 1 of 1	3
LINC02548	ENST00000531749.1 link	n.189-14528G>A	intron_variant	Intron 2 of 2	3
LINC02548	ENST00000648524.1 link	n.587-7476G>A	intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes

AF:

0.124

AC:

18922

AN:

152000

Hom.:

1594

Cov.:

show subpopulations

Gnomad AFR

AF:

0.232

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.116

Gnomad ASJ

AF:

0.171

Gnomad EAS

AF:

0.107

Gnomad SAS

AF:

0.118

Gnomad FIN

AF:

0.0250

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.0760

Gnomad OTH

AF:

0.125

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

GnomAD4 genome

AF:

0.125

AC:

18945

AN:

152116

Hom.:

1597

Cov.:

AF XY:

0.121

AC XY:

8989

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.232

AC:

9609

AN:

41450

American (AMR)

AF:

0.116

AC:

1768

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.171

AC:

592

AN:

3466

East Asian (EAS)

AF:

0.107

AC:

552

AN:

5180

South Asian (SAS)

AF:

0.117

AC:

565

AN:

4822

European-Finnish (FIN)

AF:

0.0250

AC:

265

AN:

10596

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0760

AC:

5171

AN:

68004

Other (OTH)

AF:

0.124

AC:

262

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

794

1588

2382

3176

3970

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0971

Hom.:

2775

Bravo

AF:

0.137

Asia WGS

AF:

0.128

AC:

446

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.8

(source)

DANN

Benign

0.59

PhyloP100

-0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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rs12146602

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