rs397516644
Positions:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_001330.5(CTF1):c.*5C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000124 in 1,499,584 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00013 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00012 ( 0 hom. )
Consequence
CTF1
NM_001330.5 3_prime_UTR
NM_001330.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.963
Genes affected
CTF1 (HGNC:2499): (cardiotrophin 1) The protein encoded by this gene is a secreted cytokine that induces cardiac myocyte hypertrophy in vitro. It has been shown to bind and activate the ILST/gp130 receoptor. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
Variant 16-30902544-C-A is Benign according to our data. Variant chr16-30902544-C-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 44171.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=2}.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTF1 | NM_001330.5 | c.*5C>A | 3_prime_UTR_variant | 3/3 | ENST00000279804.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTF1 | ENST00000279804.3 | c.*5C>A | 3_prime_UTR_variant | 3/3 | 1 | NM_001330.5 | P3 | ||
CTF1 | ENST00000395019.3 | c.*5C>A | 3_prime_UTR_variant | 3/3 | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152118Hom.: 0 Cov.: 31
GnomAD3 genomes
?
AF:
AC:
20
AN:
152118
Hom.:
Cov.:
31
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:
GnomAD3 exomes AF: 0.000182 AC: 20AN: 109682Hom.: 0 AF XY: 0.000209 AC XY: 13AN XY: 62214
GnomAD3 exomes
AF:
AC:
20
AN:
109682
Hom.:
AF XY:
AC XY:
13
AN XY:
62214
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000123 AC: 166AN: 1347466Hom.: 0 Cov.: 30 AF XY: 0.000128 AC XY: 85AN XY: 664616
GnomAD4 exome
AF:
AC:
166
AN:
1347466
Hom.:
Cov.:
30
AF XY:
AC XY:
85
AN XY:
664616
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152118Hom.: 0 Cov.: 31 AF XY: 0.000108 AC XY: 8AN XY: 74298
GnomAD4 genome
?
AF:
AC:
20
AN:
152118
Hom.:
Cov.:
31
AF XY:
AC XY:
8
AN XY:
74298
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:2Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 05, 2013 | The *5C>A variant in CTF1 has not been reported in the literature nor previously identified by our laboratory. This variant occurs in the 3' untranslated region (3' UTR) and does not affect the coding sequence of the gene. Additional inform ation is needed to fully assess the clinical significance of this variant. - |
Cardiomyopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario | Apr 12, 2016 | - - |
CTF1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 24, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at