dbSNP rs10507022: LINC02413:n.105-3195T>A (chr12-92987492-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000755877.1(LINC02413):n.105-3195T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.047 in 152,196 control chromosomes in the GnomAD database, including 323 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 0.047 ( 323 hom., cov: 32)

Consequence

LINC02413
ENST00000755877.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.413

Publications

2 publications found

Variant links:

Genes affected

LINC02413 (HGNC:53342): (long intergenic non-protein coding RNA 2413)

LINC02413 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=-0.67).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02413	ENST00000755877.1 link	n.105-3195T>A		intron_variant	Intron 1 of 2
LINC02413	ENST00000755878.1 link	n.199-3195T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0468

AC:

7124

AN:

152076

Hom.:

315

Cov.:

show subpopulations

Gnomad AFR

AF:

0.106

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0166

Gnomad ASJ

AF:

0.00548

Gnomad EAS

AF:

0.0400

Gnomad SAS

AF:

0.0676

Gnomad FIN

AF:

0.0611

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0178

Gnomad OTH

AF:

0.0354

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

GnomAD4 genome

AF:

0.0470

AC:

7154

AN:

152196

Hom.:

323

Cov.:

AF XY:

0.0484

AC XY:

3601

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.106

AC:

4393

AN:

41500

American (AMR)

AF:

0.0166

AC:

254

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.00548

AC:

AN:

3470

East Asian (EAS)

AF:

0.0399

AC:

207

AN:

5188

South Asian (SAS)

AF:

0.0679

AC:

327

AN:

4818

European-Finnish (FIN)

AF:

0.0611

AC:

647

AN:

10584

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0178

AC:

1213

AN:

68026

Other (OTH)

AF:

0.0435

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

328

657

985

1314

1642

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

246

328

410

<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:

0.0147

Hom.:

Bravo

AF:

0.0446

Asia WGS

AF:

0.0850

AC:

297

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

8.5

(source)

DANN

Benign

0.79

PhyloP100

0.41

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