rs11256951
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001326342.2(CELF2):c.74+14420A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,070 control chromosomes in the GnomAD database, including 14,876 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 0.42 ( 14876 hom., cov: 33)
Consequence
CELF2
NM_001326342.2 intron
NM_001326342.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.35
Publications
1 publications found
Genes affected
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 97Inheritance: AD Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
- undetermined early-onset epileptic encephalopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- complex neurodevelopmental disorderInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
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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 (NFE) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CELF2 | NM_001326342.2 | c.74+14420A>G | intron_variant | Intron 1 of 12 | ENST00000633077.2 | NP_001313271.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.425 AC: 64575AN: 151952Hom.: 14870 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
64575
AN:
151952
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.425 AC: 64601AN: 152070Hom.: 14876 Cov.: 33 AF XY: 0.415 AC XY: 30859AN XY: 74338 show subpopulations
GnomAD4 genome
AF:
AC:
64601
AN:
152070
Hom.:
Cov.:
33
AF XY:
AC XY:
30859
AN XY:
74338
show subpopulations
African (AFR)
AF:
AC:
11875
AN:
41474
American (AMR)
AF:
AC:
5538
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
AC:
1714
AN:
3470
East Asian (EAS)
AF:
AC:
695
AN:
5190
South Asian (SAS)
AF:
AC:
1580
AN:
4820
European-Finnish (FIN)
AF:
AC:
4789
AN:
10550
Middle Eastern (MID)
AF:
AC:
112
AN:
292
European-Non Finnish (NFE)
AF:
AC:
36883
AN:
67976
Other (OTH)
AF:
AC:
878
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1825
3649
5474
7298
9123
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
844
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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