Genetic Variant LINC02694:n.17C>G (chr15-38696614-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NR_160786.1(LINC02694):n.17C>G 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 0.289 in 1,611,242 control chromosomes in the GnomAD database, including 69,331 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 0.26 ( 5342 hom., cov: 32)

Exomes 𝑓: 0.29 ( 63989 hom. )

Consequence

LINC02694
NR_160786.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.656

Publications

33 publications found

Variant links:

Genes affected

LINC02694 (HGNC:33796): (long intergenic non-protein coding RNA 2694)

LINC02694 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=0.005088091).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_160786.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02694	NR_160786.1		n.17C>G		non_coding_transcript_exon	Exon 1 of 2

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
LINC02694	ENST00000643127.1	n.17C>G	non_coding_transcript_exon	Exon 1 of 2
LINC02694	ENST00000645994.2	n.130C>G	non_coding_transcript_exon	Exon 1 of 3
LINC02694	ENST00000831755.1	n.34C>G	non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.257

AC:

39063

AN:

152010

Hom.:

5342

Cov.:

show subpopulations

Gnomad AFR

AF:

0.196

Gnomad AMI

AF:

0.269

Gnomad AMR

AF:

0.269

Gnomad ASJ

AF:

0.316

Gnomad EAS

AF:

0.0939

Gnomad SAS

AF:

0.207

Gnomad FIN

AF:

0.258

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.303

Gnomad OTH

AF:

0.281

GnomAD2 exomes

AF:

0.264

AC:

66097

AN:

250414

AF XY:

0.266

show subpopulations

Gnomad AFR exome

AF:

0.192

Gnomad AMR exome

AF:

0.261

Gnomad ASJ exome

AF:

0.317

Gnomad EAS exome

AF:

0.0937

Gnomad FIN exome

AF:

0.262

Gnomad NFE exome

AF:

0.309

Gnomad OTH exome

AF:

0.292

GnomAD4 exome

AF:

0.292

AC:

425924

AN:

1459114

Hom.:

63989

Cov.:

AF XY:

0.291

AC XY:

211332

AN XY:

725970

show subpopulations

African (AFR)

AF:

0.203

AC:

6763

AN:

33382

American (AMR)

AF:

0.265

AC:

11795

AN:

44584

Ashkenazi Jewish (ASJ)

AF:

0.312

AC:

8121

AN:

26052

East Asian (EAS)

AF:

0.0968

AC:

3842

AN:

39690

South Asian (SAS)

AF:

0.224

AC:

19257

AN:

86152

European-Finnish (FIN)

AF:

0.257

AC:

13742

AN:

53372

Middle Eastern (MID)

AF:

0.318

AC:

1819

AN:

5722

European-Non Finnish (NFE)

AF:

0.309

AC:

343504

AN:

1109874

Other (OTH)

AF:

0.283

AC:

17081

AN:

60286

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.451

Heterozygous variant carriers

13895

27790

41686

55581

69476

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11092

22184

33276

44368

55460

<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:

0.257

AC:

39086

AN:

152128

Hom.:

5342

Cov.:

AF XY:

0.255

AC XY:

18950

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.196

AC:

8123

AN:

41508

American (AMR)

AF:

0.269

AC:

4111

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.316

AC:

1098

AN:

3470

East Asian (EAS)

AF:

0.0943

AC:

489

AN:

5184

South Asian (SAS)

AF:

0.206

AC:

994

AN:

4816

European-Finnish (FIN)

AF:

0.258

AC:

2726

AN:

10576

Middle Eastern (MID)

AF:

0.316

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.303

AC:

20619

AN:

67960

Other (OTH)

AF:

0.278

AC:

588

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1493

2986

4479

5972

7465

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

414

828

1242

1656

2070

<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:

0.283

Hom.:

4821

Bravo

AF:

0.261

TwinsUK

AF:

0.316

AC:

1172

ALSPAC

AF:

0.313

AC:

1207

ESP6500AA

AF:

0.208

AC:

917

ESP6500EA

AF:

0.303

AC:

2604

ExAC

AF:

0.263

AC:

31869

Asia WGS

AF:

0.152

AC:

526

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.79

BayesDel_noAF

Benign

-0.76

CADD

Benign

0.77

(source)

DANN

Benign

0.87

DEOGEN2

Benign

0.064

Eigen

Benign

-0.84

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.035

LIST_S2

Benign

0.35

MetaRNN

Benign

0.0051

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.0

PhyloP100

-0.66

PROVEAN

Benign

-2.0

REVEL

Benign

0.10

Sift4G

Pathogenic

0.0

Polyphen

0.97

Vest4

0.027

MPC

0.059

ClinPred

0.014

GERP RS

-0.56

Varity_R

0.29

gMVP

0.0075

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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