rs11256951

Variant summary

Our verdict is Benign. Variant got -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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.35
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE UniProt
CELF2NM_001326342.2 linkuse as main transcriptc.74+14420A>G intron_variant ENST00000633077.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CELF2ENST00000633077.2 linkuse as main transcriptc.74+14420A>G intron_variant 1 NM_001326342.2 P1

Frequencies

GnomAD3 genomes
AF:
0.425
AC:
64575
AN:
151952
Hom.:
14870
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.286
Gnomad AMI
AF:
0.591
Gnomad AMR
AF:
0.363
Gnomad ASJ
AF:
0.494
Gnomad EAS
AF:
0.134
Gnomad SAS
AF:
0.328
Gnomad FIN
AF:
0.454
Gnomad MID
AF:
0.385
Gnomad NFE
AF:
0.543
Gnomad OTH
AF:
0.418
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.425
AC:
64601
AN:
152070
Hom.:
14876
Cov.:
33
AF XY:
0.415
AC XY:
30859
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.286
Gnomad4 AMR
AF:
0.362
Gnomad4 ASJ
AF:
0.494
Gnomad4 EAS
AF:
0.134
Gnomad4 SAS
AF:
0.328
Gnomad4 FIN
AF:
0.454
Gnomad4 NFE
AF:
0.543
Gnomad4 OTH
AF:
0.416
Alfa
AF:
0.506
Hom.:
13026
Bravo
AF:
0.412
Asia WGS
AF:
0.242
AC:
844
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.0020
DANN
Benign
0.39

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs11256951; hg19: chr10-11074546; API