10-10940683-C-T

Variant summary

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

The ENST00000428520.7(LINC00710):​n.687+3500G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,978 control chromosomes in the GnomAD database, including 10,042 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 0.35 ( 10042 hom., cov: 32)

Consequence

LINC00710
ENST00000428520.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.569

Publications

2 publications found
Variant links:
Genes affected
LINC00710 (HGNC:27386): (long intergenic non-protein coding RNA 710)
CELF2 (HGNC:2550): (CUGBP Elav-like family member 2) Members of the CELF/BRUNOL protein family contain two N-terminal RNA recognition motif (RRM) domains, one C-terminal RRM domain, and a divergent segment of 160-230 aa between the second and third RRM domains. Members of this protein family regulate pre-mRNA alternative splicing and may also be involved in mRNA editing, and translation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
CELF2 Gene-Disease associations (from GenCC):
  • developmental and epileptic encephalopathy 97
    Inheritance: AD Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
  • undetermined early-onset epileptic encephalopathy
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • complex neurodevelopmental disorder
    Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

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=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CELF2NM_001326325.2 linkc.146+20684C>T intron_variant Intron 3 of 15 NP_001313254.1
CELF2NM_001326327.2 linkc.89+20684C>T intron_variant Intron 2 of 14 NP_001313256.1
CELF2NM_001326326.2 linkc.89+20684C>T intron_variant Intron 2 of 14 NP_001313255.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC00710ENST00000428520.7 linkn.687+3500G>A intron_variant Intron 5 of 5 1
LINC00710ENST00000635670.2 linkn.455+3500G>A intron_variant Intron 3 of 4 1
CELF2ENST00000637215.1 linkc.89+20684C>T intron_variant Intron 2 of 14 5 ENSP00000490185.1 A0A1B0GUN8

Frequencies

GnomAD3 genomes
AF:
0.346
AC:
52577
AN:
151862
Hom.:
10030
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.257
Gnomad AMI
AF:
0.209
Gnomad AMR
AF:
0.499
Gnomad ASJ
AF:
0.299
Gnomad EAS
AF:
0.733
Gnomad SAS
AF:
0.501
Gnomad FIN
AF:
0.428
Gnomad MID
AF:
0.339
Gnomad NFE
AF:
0.317
Gnomad OTH
AF:
0.370
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.346
AC:
52628
AN:
151978
Hom.:
10042
Cov.:
32
AF XY:
0.359
AC XY:
26681
AN XY:
74296
show subpopulations
African (AFR)
AF:
0.257
AC:
10663
AN:
41446
American (AMR)
AF:
0.500
AC:
7630
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
0.299
AC:
1038
AN:
3468
East Asian (EAS)
AF:
0.734
AC:
3788
AN:
5162
South Asian (SAS)
AF:
0.499
AC:
2404
AN:
4816
European-Finnish (FIN)
AF:
0.428
AC:
4514
AN:
10542
Middle Eastern (MID)
AF:
0.342
AC:
100
AN:
292
European-Non Finnish (NFE)
AF:
0.316
AC:
21508
AN:
67964
Other (OTH)
AF:
0.375
AC:
793
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1674
3348
5023
6697
8371
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
528
1056
1584
2112
2640
<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:
0.328
Hom.:
6270
Bravo
AF:
0.347
Asia WGS
AF:
0.591
AC:
2050
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.42
DANN
Benign
0.20
PhyloP100
-0.57

Splicing

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

Publications

Other links and lift over

dbSNP: rs10795839; hg19: chr10-10982646; API