chr16-30899474-CAGA-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_001330.5(CTF1):c.86_88del(p.Gln29_Thr30delinsPro) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.000000684 in 1,461,160 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
CTF1
NM_001330.5 inframe_deletion
NM_001330.5 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.63
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Nonframeshift variant in NON repetitive region in NM_001330.5. Strenght limited to Supporting due to length of the change: 1aa.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTF1 | NM_001330.5 | c.86_88del | p.Gln29_Thr30delinsPro | inframe_deletion | 2/3 | ENST00000279804.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTF1 | ENST00000279804.3 | c.86_88del | p.Gln29_Thr30delinsPro | inframe_deletion | 2/3 | 1 | NM_001330.5 | P3 | |
CTF1 | ENST00000395019.3 | c.83_85del | p.Gln28_Thr29delinsPro | inframe_deletion | 2/3 | 1 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461160Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 726882
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
Bravo
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Dilated Cardiomyopathy, Dominant Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 05, 2021 | This variant, c.86_88del, is a complex sequence change that results in the deletion of 2 and insertion of 1 amino acid(s) in the CTF1 protein (p.Gln29_Thr30delinsPro). This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with CTF1-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at