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

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

2

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)

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=-0.91).
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 HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC02682ENST00000664116.1 linkn.872-9C>T intron_variant Intron 8 of 8
LINC02682ENST00000757694.1 linkn.478-9C>T intron_variant Intron 4 of 4
LINC02682ENST00000757695.1 linkn.291-9C>T intron_variant Intron 3 of 3

Frequencies

GnomAD3 genomes
AF:
0.0600
AC:
9124
AN:
152124
Hom.:
867
Cov.:
32
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.:
32
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:
14
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
0
373
747
1120
1494
1867
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
112
224
336
448
560
<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:
0.0622
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
DANN
Benign
0.41
PhyloP100
-0.71

Splicing

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

Publications

Other links and lift over

dbSNP: rs11023787; hg19: chr11-15952294; API