dbSNP rs4905757: LINC02914:n.340T>C (chr14-98716289-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000541516.1(LINC02914):n.340T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0458 in 1,614,048 control chromosomes in the GnomAD database, including 2,258 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 0.038 ( 177 hom., cov: 32)

Exomes 𝑓: 0.047 ( 2081 hom. )

Consequence

LINC02914
ENST00000541516.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0660

Publications

12 publications found

Variant links:

Genes affected

LINC02914 (HGNC:26375): (long intergenic non-protein coding RNA 2914)

LINC02914 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 (MetaRNN=0.0022147).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0509 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000541516.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
LINC02914	NR_161367.1	n.649T>C	non_coding_transcript_exon	Exon 4 of 5
LINC02914	NR_161368.1	n.517T>C	non_coding_transcript_exon	Exon 3 of 4
LINC02914	NR_161369.1	n.347T>C	non_coding_transcript_exon	Exon 2 of 3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
LINC02914	ENST00000541516.1	TSL:3	n.340T>C	non_coding_transcript_exon	Exon 2 of 3
LINC02914	ENST00000650364.1		n.517T>C	non_coding_transcript_exon	Exon 3 of 4
LINC02914	ENST00000546029.2	TSL:2	n.*116T>C	downstream_gene	N/A

Frequencies

GnomAD3 genomes

AF:

0.0376

AC:

5720

AN:

152142

Hom.:

177

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00960

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.0341

Gnomad ASJ

AF:

0.0818

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0124

Gnomad FIN

AF:

0.0630

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0524

Gnomad OTH

AF:

0.0421

GnomAD2 exomes

AF:

0.0388

AC:

9741

AN:

250956

AF XY:

0.0393

show subpopulations

Gnomad AFR exome

AF:

0.00752

Gnomad AMR exome

AF:

0.0251

Gnomad ASJ exome

AF:

0.0906

Gnomad EAS exome

AF:

0.0000544

Gnomad FIN exome

AF:

0.0565

Gnomad NFE exome

AF:

0.0520

Gnomad OTH exome

AF:

0.0464

GnomAD4 exome

AF:

0.0467

AC:

68195

AN:

1461788

Hom.:

2081

Cov.:

AF XY:

0.0458

AC XY:

33335

AN XY:

727184

show subpopulations

African (AFR)

AF:

0.00818

AC:

274

AN:

33480

American (AMR)

AF:

0.0265

AC:

1187

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.0896

AC:

2342

AN:

26136

East Asian (EAS)

AF:

0.0000756

AC:

AN:

39698

South Asian (SAS)

AF:

0.0142

AC:

1224

AN:

86254

European-Finnish (FIN)

AF:

0.0534

AC:

2851

AN:

53418

Middle Eastern (MID)

AF:

0.0602

AC:

347

AN:

5768

European-Non Finnish (NFE)

AF:

0.0514

AC:

57203

AN:

1111924

Other (OTH)

AF:

0.0458

AC:

2764

AN:

60392

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

4007

8014

12021

16028

20035

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2052

4104

6156

8208

10260

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0376

AC:

5723

AN:

152260

Hom.:

177

Cov.:

AF XY:

0.0375

AC XY:

2796

AN XY:

74462

show subpopulations

African (AFR)

AF:

0.00958

AC:

398

AN:

41566

American (AMR)

AF:

0.0340

AC:

519

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0818

AC:

284

AN:

3472

East Asian (EAS)

AF:

0.000580

AC:

AN:

5176

South Asian (SAS)

AF:

0.0131

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.0630

AC:

668

AN:

10610

Middle Eastern (MID)

AF:

0.0782

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0524

AC:

3562

AN:

68010

Other (OTH)

AF:

0.0417

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

286

572

859

1145

1431

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

140

210

280

350

<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:

0.0486

Hom.:

724

Bravo

AF:

0.0349

TwinsUK

AF:

0.0574

AC:

213

ALSPAC

AF:

0.0509

AC:

196

ESP6500AA

AF:

0.00749

AC:

ESP6500EA

AF:

0.0538

AC:

463

ExAC

AF:

0.0372

AC:

4522

Asia WGS

AF:

0.00751

AC:

AN:

3478

EpiCase

AF:

0.0547

EpiControl

AF:

0.0542

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.19

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.66

CADD

Benign

1.1

(source)

DANN

Benign

0.47

DEOGEN2

Benign

0.053

Eigen

Benign

-0.90

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.024

LIST_S2

Benign

0.25

MetaRNN

Benign

0.0022

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.0

PhyloP100

-0.066

PROVEAN

Uncertain

-4.0

REVEL

Benign

0.058

Polyphen

0.50

Vest4

0.077

MPC

0.0099

ClinPred

0.055

GERP RS

-0.47

Varity_R

0.43

gMVP

0.0021

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over