chr11-113323102-CA-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_017868.4(TTC12):c.59-167del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0185 in 79,444 control chromosomes in the GnomAD database, including 10 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.019 ( 10 hom., cov: 23)
Consequence
TTC12
NM_017868.4 intron
NM_017868.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.19
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 -10 ACMG points.
BP6
?
Variant 11-113323102-CA-C is Benign according to our data. Variant chr11-113323102-CA-C is described in ClinVar as [Benign]. Clinvar id is 1225031.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0185 (1470/79444) while in subpopulation AFR AF= 0.0401 (787/19632). AF 95% confidence interval is 0.0378. There are 10 homozygotes in gnomad4. There are 732 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 10 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC12 | NM_017868.4 | c.59-167del | intron_variant | ENST00000529221.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC12 | ENST00000529221.6 | c.59-167del | intron_variant | 2 | NM_017868.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0184 AC: 1464AN: 79438Hom.: 10 Cov.: 23
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0185 AC: 1470AN: 79444Hom.: 10 Cov.: 23 AF XY: 0.0197 AC XY: 732AN XY: 37154
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?
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 19, 2021 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at