10-11013626-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001326325.2(CELF2):​c.146+93627T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.869 in 152,204 control chromosomes in the GnomAD database, including 58,502 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 0.87 ( 58502 hom., cov: 32)

Consequence

CELF2
NM_001326325.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.971
Variant links:
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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CELF2NM_001326325.2 linkc.146+93627T>C intron_variant Intron 3 of 15 NP_001313254.1
CELF2NM_001326336.2 linkc.53+8186T>C intron_variant Intron 1 of 13 NP_001313265.1
CELF2NM_001326327.2 linkc.89+93627T>C intron_variant Intron 2 of 14 NP_001313256.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CELF2ENST00000416382.6 linkc.53+8186T>C intron_variant Intron 1 of 12 1 ENSP00000406451.2 O95319-1
CELF2ENST00000637215.1 linkc.89+93627T>C intron_variant Intron 2 of 14 5 ENSP00000490185.1 A0A1B0GUN8
CELF2ENST00000636488.1 linkc.89+93627T>C intron_variant Intron 2 of 13 5 ENSP00000489955.1 A0A1B0GU44

Frequencies

GnomAD3 genomes
AF:
0.869
AC:
132193
AN:
152086
Hom.:
58460
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.689
Gnomad AMI
AF:
0.911
Gnomad AMR
AF:
0.914
Gnomad ASJ
AF:
0.922
Gnomad EAS
AF:
0.999
Gnomad SAS
AF:
0.979
Gnomad FIN
AF:
0.978
Gnomad MID
AF:
0.861
Gnomad NFE
AF:
0.930
Gnomad OTH
AF:
0.879
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.869
AC:
132289
AN:
152204
Hom.:
58502
Cov.:
32
AF XY:
0.874
AC XY:
65066
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.689
Gnomad4 AMR
AF:
0.914
Gnomad4 ASJ
AF:
0.922
Gnomad4 EAS
AF:
0.999
Gnomad4 SAS
AF:
0.979
Gnomad4 FIN
AF:
0.978
Gnomad4 NFE
AF:
0.930
Gnomad4 OTH
AF:
0.880
Alfa
AF:
0.920
Hom.:
81740
Bravo
AF:
0.856
Asia WGS
AF:
0.981
AC:
3412
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.27
DANN
Benign
0.33

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1547221; hg19: chr10-11055589; API