11-113363957-T-C
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_017868.4(TTC12):c.1816+30T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 1,509,252 control chromosomes in the GnomAD database, including 269,872 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.54 ( 23090 hom., cov: 34)
Exomes 𝑓: 0.60 ( 246782 hom. )
Consequence
TTC12
NM_017868.4 intron
NM_017868.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.15
Genes affected
TTC12 (HGNC:23700): (tetratricopeptide repeat domain 12) Involved in axonemal dynein complex assembly and sperm axoneme assembly. Located in centrosome and cytoplasm. Implicated in primary ciliary dyskinesia 45. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 11-113363957-T-C is Benign according to our data. Variant chr11-113363957-T-C is described in ClinVar as [Benign]. Clinvar id is 1280036.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TTC12 | NM_017868.4 | c.1816+30T>C | intron_variant | ENST00000529221.6 | NP_060338.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TTC12 | ENST00000529221.6 | c.1816+30T>C | intron_variant | 2 | NM_017868.4 | ENSP00000433757.1 |
Frequencies
GnomAD3 genomes AF: 0.541 AC: 82283AN: 152096Hom.: 23083 Cov.: 34
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GnomAD3 exomes AF: 0.565 AC: 136094AN: 240964Hom.: 39409 AF XY: 0.574 AC XY: 74710AN XY: 130084
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GnomAD4 exome AF: 0.600 AC: 813611AN: 1357038Hom.: 246782 Cov.: 19 AF XY: 0.600 AC XY: 408048AN XY: 680288
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GnomAD4 genome AF: 0.541 AC: 82324AN: 152214Hom.: 23090 Cov.: 34 AF XY: 0.541 AC XY: 40270AN XY: 74412
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 15, 2021 | - - |
Ciliary dyskinesia, primary, 45 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 10, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
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