Genetic Variant ENST00000664116.1:n.872-9C>T (chr11-15930748-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000664116.1(LINC02682):n.872-9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0599 in 152,242 control chromosomes in the GnomAD database, including 868 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 0.060 ( 868 hom., cov: 32)

Consequence

LINC02682
ENST00000664116.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.715

Publications

14 publications found

Variant links:

Genes affected

LINC02682 (HGNC:54177): (long intergenic non-protein coding RNA 2682)

LINC02682 links:

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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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02682	ENST00000664116.1 link	n.872-9C>T	intron_variant	Intron 8 of 8
LINC02682	ENST00000757694.1 link	n.478-9C>T	intron_variant	Intron 4 of 4
LINC02682	ENST00000757695.1 link	n.291-9C>T	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0600

AC:

9124

AN:

152124

Hom.:

867

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0186

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.0733

Gnomad ASJ

AF:

0.0683

Gnomad EAS

AF:

0.492

Gnomad SAS

AF:

0.174

Gnomad FIN

AF:

0.0512

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0427

Gnomad OTH

AF:

0.0707

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

GnomAD4 genome

AF:

0.0599

AC:

9125

AN:

152242

Hom.:

868

Cov.:

AF XY:

0.0647

AC XY:

4814

AN XY:

74428

show subpopulations

African (AFR)

AF:

0.0186

AC:

773

AN:

41562

American (AMR)

AF:

0.0735

AC:

1124

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0683

AC:

237

AN:

3472

East Asian (EAS)

AF:

0.492

AC:

2534

AN:

5148

South Asian (SAS)

AF:

0.173

AC:

832

AN:

4808

European-Finnish (FIN)

AF:

0.0512

AC:

543

AN:

10610

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0427

AC:

2905

AN:

68020

Other (OTH)

AF:

0.0738

AC:

156

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

373

747

1120

1494

1867

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0622

Hom.:

1515

Bravo

AF:

0.0611

Asia WGS

AF:

0.285

AC:

989

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.75

(source)

DANN

Benign

0.41

PhyloP100

-0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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ENST00000664116.1:n.872-9C>T

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