dbSNP rs12912251: LINC02694:n.96+66012G>T (chr15-38694167-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000644461.1(LINC02694):n.96+66012G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,150 control chromosomes in the GnomAD database, including 5,079 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 0.25 ( 5079 hom., cov: 32)

Consequence

LINC02694
ENST00000644461.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0860

Publications

24 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 (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02694	ENST00000644461.1 link	n.96+66012G>T	intron_variant	Intron 1 of 4
LINC02694	ENST00000646232.1 link	n.163+4853G>T	intron_variant	Intron 2 of 3
LINC02694	ENST00000647456.1 link	n.572+4853G>T	intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes

AF:

0.249

AC:

37864

AN:

152032

Hom.:

5078

Cov.:

show subpopulations

Gnomad AFR

AF:

0.172

Gnomad AMI

AF:

0.268

Gnomad AMR

AF:

0.265

Gnomad ASJ

AF:

0.313

Gnomad EAS

AF:

0.0946

Gnomad SAS

AF:

0.203

Gnomad FIN

AF:

0.256

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.302

Gnomad OTH

AF:

0.273

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

GnomAD4 genome

AF:

0.249

AC:

37885

AN:

152150

Hom.:

5079

Cov.:

AF XY:

0.247

AC XY:

18369

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.172

AC:

7141

AN:

41506

American (AMR)

AF:

0.265

AC:

4053

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.313

AC:

1087

AN:

3472

East Asian (EAS)

AF:

0.0948

AC:

491

AN:

5178

South Asian (SAS)

AF:

0.203

AC:

978

AN:

4820

European-Finnish (FIN)

AF:

0.256

AC:

2706

AN:

10580

Middle Eastern (MID)

AF:

0.313

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.302

AC:

20522

AN:

67982

Other (OTH)

AF:

0.270

AC:

571

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1458

2916

4373

5831

7289

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

406

812

1218

1624

2030

<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:

0.287

Hom.:

18940

Bravo

AF:

0.252

Asia WGS

AF:

0.148

AC:

512

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

1.7

(source)

DANN

Benign

0.75

PhyloP100

0.086

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