rs397516645
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_001330.5(CTF1):c.145-10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000827 in 1,450,354 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 0.000040 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000046 ( 0 hom. )
Consequence
CTF1
NM_001330.5 intron
NM_001330.5 intron
Scores
2
Splicing: ADA: 0.8673
2
Clinical Significance
Conservation
PhyloP100: 0.756
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 Likely_benign. Variant got -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
Variant 16-30902068-G-A is Benign according to our data. Variant chr16-30902068-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 44174.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Likely_benign=1}.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 151850Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000487 AC: 4AN: 82074Hom.: 0 AF XY: 0.0000641 AC XY: 3AN XY: 46798
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GnomAD4 exome AF: 0.00000462 AC: 6AN: 1298504Hom.: 0 Cov.: 30 AF XY: 0.00000312 AC XY: 2AN XY: 640348
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GnomAD4 genome AF: 0.0000395 AC: 6AN: 151850Hom.: 0 Cov.: 31 AF XY: 0.0000539 AC XY: 4AN XY: 74174
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign: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 | May 01, 2012 | Variant classified as Uncertain Significance - Favor Benign. The 145-10G>A varia nt (CTF1) has not been reported in the literature nor previously identified by o ur laboratory. This variant is located in the 3' splice region. Computational to ols do not predict altered splicing; however, this information is not predictive enough to rule out pathogenicity. Additional studies are needed to fully assess the clinical significance of the 145-10G>A variant. - |
Dilated Cardiomyopathy, Dominant Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 21, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at