rs7099713
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001326325.2(CELF2):c.146+91181A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0656 in 152,220 control chromosomes in the GnomAD database, including 354 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 0.066 ( 354 hom., cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CELF2
NM_001326325.2 intron
NM_001326325.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.595
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 made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0772 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CELF2 | NM_001326325.2 | c.146+91181A>C | intron_variant | Intron 3 of 15 | NP_001313254.1 | |||
CELF2 | NM_001326336.2 | c.53+5740A>C | intron_variant | Intron 1 of 13 | NP_001313265.1 | |||
CELF2 | NM_001326327.2 | c.89+91181A>C | intron_variant | Intron 2 of 14 | NP_001313256.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CELF2 | ENST00000416382.6 | c.53+5740A>C | intron_variant | Intron 1 of 12 | 1 | ENSP00000406451.2 | ||||
CELF2 | ENST00000637215.1 | c.89+91181A>C | intron_variant | Intron 2 of 14 | 5 | ENSP00000490185.1 | ||||
CELF2 | ENST00000636488.1 | c.89+91181A>C | intron_variant | Intron 2 of 13 | 5 | ENSP00000489955.1 |
Frequencies
GnomAD3 genomes AF: 0.0656 AC: 9972AN: 152102Hom.: 353 Cov.: 31
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31
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 8Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 6
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GnomAD4 genome AF: 0.0656 AC: 9980AN: 152220Hom.: 354 Cov.: 31 AF XY: 0.0623 AC XY: 4638AN XY: 74426
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at