chr3-180605796-T-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_133462.4(TTC14):c.888T>C(p.Ser296=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000422 in 1,570,098 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 0.0025 ( 5 hom., cov: 33)
Exomes 𝑓: 0.00020 ( 2 hom. )
Consequence
TTC14
NM_133462.4 synonymous
NM_133462.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.720
Genes affected
TTC14 (HGNC:24697): (tetratricopeptide repeat domain 14) Predicted to enable nucleic acid binding activity. [provided by Alliance of Genome Resources, Apr 2022]
CCDC39 (HGNC:25244): (coiled-coil domain 39 molecular ruler complex subunit) The protein encoded by this gene is involved in the motility of cilia and flagella. The encoded protein is essential for the assembly of dynein regulatory and inner dynein arm complexes, which regulate ciliary beat. Defects in this gene are a cause of primary ciliary dyskinesia type 14 (CILD14). [provided by RefSeq, Jul 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
?
Variant 3-180605796-T-C is Benign according to our data. Variant chr3-180605796-T-C is described in ClinVar as [Benign]. Clinvar id is 3050662.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.72 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC14 | NM_133462.4 | c.888T>C | p.Ser296= | synonymous_variant | 7/12 | ENST00000296015.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC14 | ENST00000296015.9 | c.888T>C | p.Ser296= | synonymous_variant | 7/12 | 1 | NM_133462.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00253 AC: 385AN: 152226Hom.: 5 Cov.: 33
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GnomAD3 exomes AF: 0.000714 AC: 148AN: 207376Hom.: 3 AF XY: 0.000493 AC XY: 56AN XY: 113562
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GnomAD4 exome AF: 0.000195 AC: 277AN: 1417754Hom.: 2 Cov.: 30 AF XY: 0.000176 AC XY: 124AN XY: 705442
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
TTC14-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 12, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
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Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at