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11-47472254-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_001376376.1(CELF1):c.1521G>A(p.Ser507=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00211 in 1,614,156 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0019 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0021 ( 6 hom. )

Consequence

CELF1
NM_001376376.1 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0270
Variant links:
Genes affected
CELF1 (HGNC:2549): (CUGBP Elav-like family member 1) 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. This gene may play a role in myotonic dystrophy type 1 (DM1) via interactions with the dystrophia myotonica-protein kinase (DMPK) gene. 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 -9 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.29).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-47472254-C-T is Benign according to our data. Variant chr11-47472254-C-T is described in ClinVar as [Benign]. Clinvar id is 791545.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.027 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 295 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CELF1NM_001376376.1 linkuse as main transcriptc.1521G>A p.Ser507= synonymous_variant 15/15 ENST00000687097.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CELF1ENST00000687097.1 linkuse as main transcriptc.1521G>A p.Ser507= synonymous_variant 15/15 NM_001376376.1 P3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00194
AC:
295
AN:
152206
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000338
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00131
Gnomad ASJ
AF:
0.0107
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00290
Gnomad FIN
AF:
0.000565
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.00276
Gnomad OTH
AF:
0.00478
GnomAD3 exomes
AF:
0.00242
AC:
608
AN:
251388
Hom.:
1
AF XY:
0.00259
AC XY:
352
AN XY:
135856
show subpopulations
Gnomad AFR exome
AF:
0.000431
Gnomad AMR exome
AF:
0.000723
Gnomad ASJ exome
AF:
0.0103
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00327
Gnomad FIN exome
AF:
0.00115
Gnomad NFE exome
AF:
0.00293
Gnomad OTH exome
AF:
0.00228
GnomAD4 exome
AF:
0.00213
AC:
3115
AN:
1461832
Hom.:
6
Cov.:
30
AF XY:
0.00219
AC XY:
1596
AN XY:
727218
show subpopulations
Gnomad4 AFR exome
AF:
0.000388
Gnomad4 AMR exome
AF:
0.000805
Gnomad4 ASJ exome
AF:
0.0101
Gnomad4 EAS exome
AF:
0.000176
Gnomad4 SAS exome
AF:
0.00292
Gnomad4 FIN exome
AF:
0.00103
Gnomad4 NFE exome
AF:
0.00207
Gnomad4 OTH exome
AF:
0.00224
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00194
AC:
295
AN:
152324
Hom.:
1
Cov.:
32
AF XY:
0.00196
AC XY:
146
AN XY:
74486
show subpopulations
Gnomad4 AFR
AF:
0.000337
Gnomad4 AMR
AF:
0.00131
Gnomad4 ASJ
AF:
0.0107
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00290
Gnomad4 FIN
AF:
0.000565
Gnomad4 NFE
AF:
0.00276
Gnomad4 OTH
AF:
0.00473
Alfa
AF:
0.00325
Hom.:
0
Bravo
AF:
0.00175
Asia WGS
AF:
0.00346
AC:
12
AN:
3478
EpiCase
AF:
0.00344
EpiControl
AF:
0.00344

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeApr 06, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.29
Cadd
Benign
12
Dann
Benign
0.67
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs145495807; hg19: chr11-47493806; API