rs2031339
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001326319.2(CELF2):c.-133+82014T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,176 control chromosomes in the GnomAD database, including 8,822 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 0.33 ( 8822 hom., cov: 34)
Consequence
CELF2
NM_001326319.2 intron
NM_001326319.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0420
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]
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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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CELF2 | NM_001326319.2 | c.-133+82014T>C | intron_variant | Intron 1 of 16 | NP_001313248.1 | |||
CELF2 | NM_001326323.2 | c.-189+82014T>C | intron_variant | Intron 1 of 17 | NP_001313252.1 | |||
CELF2 | NM_001326321.2 | c.-95+82014T>C | intron_variant | Intron 1 of 15 | NP_001313250.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|
Frequencies
GnomAD3 genomes AF: 0.326 AC: 49620AN: 152058Hom.: 8827 Cov.: 34 show subpopulations
GnomAD3 genomes
AF:
AC:
49620
AN:
152058
Hom.:
Cov.:
34
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: 0.326 AC: 49623AN: 152176Hom.: 8822 Cov.: 34 AF XY: 0.325 AC XY: 24143AN XY: 74396 show subpopulations
GnomAD4 genome
AF:
AC:
49623
AN:
152176
Hom.:
Cov.:
34
AF XY:
AC XY:
24143
AN XY:
74396
Gnomad4 AFR
AF:
AC:
0.203578
AN:
0.203578
Gnomad4 AMR
AF:
AC:
0.309514
AN:
0.309514
Gnomad4 ASJ
AF:
AC:
0.374856
AN:
0.374856
Gnomad4 EAS
AF:
AC:
0.151989
AN:
0.151989
Gnomad4 SAS
AF:
AC:
0.291391
AN:
0.291391
Gnomad4 FIN
AF:
AC:
0.39745
AN:
0.39745
Gnomad4 NFE
AF:
AC:
0.403981
AN:
0.403981
Gnomad4 OTH
AF:
AC:
0.339015
AN:
0.339015
Heterozygous variant carriers
0
1681
3363
5044
6726
8407
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
492
984
1476
1968
2460
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
849
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at