rs2276446
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS1
The ENST00000314756.7(TTC12):c.*120+284G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00211 in 528,408 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00070 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0027 ( 20 hom. )
Consequence
TTC12
ENST00000314756.7 intron
ENST00000314756.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.260
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 -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000703 (107/152268) while in subpopulation EAS AF= 0.0183 (95/5178). AF 95% confidence interval is 0.0154. There are 0 homozygotes in gnomad4. There are 59 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC12 | NR_165393.1 | n.2027G>C | non_coding_transcript_exon_variant | 17/17 | |||
TTC12 | NR_147891.2 | n.2370+284G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000602900.1 | n.270G>C | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.000703 AC: 107AN: 152150Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00267 AC: 1006AN: 376140Hom.: 20 Cov.: 0 AF XY: 0.00259 AC XY: 507AN XY: 195730
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GnomAD4 genome ? AF: 0.000703 AC: 107AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.000792 AC XY: 59AN XY: 74470
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at