dbSNP rs10498284: LINC02306:n.537+16755C>T (chr14-25819095-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 ENST00000546412.2(LINC02306):n.537+16755C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 151,960 control chromosomes in the GnomAD database, including 4,285 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 0.19 ( 4285 hom., cov: 32)

Consequence

LINC02306
ENST00000546412.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.497

Publications

1 publications found

Variant links:

Genes affected

LINC02306 (HGNC:53225): (long intergenic non-protein coding RNA 2306)

LINC02306 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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02306	ENST00000546412.2 link	n.537+16755C>T	intron_variant	Intron 5 of 9	3
LINC02306	ENST00000657312.2 link	n.959+16790C>T	intron_variant	Intron 6 of 6
LINC02306	ENST00000736904.1 link	n.279+16755C>T	intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes

AF:

0.186

AC:

28262

AN:

151842

Hom.:

4265

Cov.:

show subpopulations

Gnomad AFR

AF:

0.419

Gnomad AMI

AF:

0.0230

Gnomad AMR

AF:

0.152

Gnomad ASJ

AF:

0.0971

Gnomad EAS

AF:

0.178

Gnomad SAS

AF:

0.200

Gnomad FIN

AF:

0.0813

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.0766

Gnomad OTH

AF:

0.159

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

GnomAD4 genome

AF:

0.186

AC:

28332

AN:

151960

Hom.:

4285

Cov.:

AF XY:

0.187

AC XY:

13854

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.419

AC:

17333

AN:

41400

American (AMR)

AF:

0.152

AC:

2318

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.0971

AC:

337

AN:

3470

East Asian (EAS)

AF:

0.178

AC:

920

AN:

5164

South Asian (SAS)

AF:

0.199

AC:

959

AN:

4818

European-Finnish (FIN)

AF:

0.0813

AC:

860

AN:

10584

Middle Eastern (MID)

AF:

0.133

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0766

AC:

5202

AN:

67944

Other (OTH)

AF:

0.163

AC:

343

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1006

2012

3019

4025

5031

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

282

564

846

1128

1410

<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:

0.131

Hom.:

3587

Bravo

AF:

0.201

Asia WGS

AF:

0.214

AC:

745

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

7.4

(source)

DANN

Benign

0.32

PhyloP100

0.50

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