rs2273581
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_206996.4(SPAG17):c.*170G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0336 in 770,682 control chromosomes in the GnomAD database, including 1,467 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 0.063 ( 721 hom., cov: 32)
Exomes 𝑓: 0.026 ( 746 hom. )
Consequence
SPAG17
NM_206996.4 3_prime_UTR
NM_206996.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.422
Genes affected
SPAG17 (HGNC:26620): (sperm associated antigen 17) This gene encodes a central pair protein present in the axonemes of cells with a "9 + 2" organization of microtubules. The encoded protein is required for the proper function of the axoneme. Mutations in the orthologous gene in mice lead to primary ciliary dyskinesia characterized by immotile nasal and tracheal cilia, reduced clearance of nasal mucus, profound respiratory distress, hydrocephalus, and neonatal lethality within twelve hours of birth due to impaired airway mucociliary clearance. Single-nucleotide polymorphisms in this gene are associated with human height and targeted mutations lead to skeletal malformations affecting the limbs in mice, suggesting a role for this gene in skeletal development. [provided by RefSeq, Feb 2017]
WDR3 (HGNC:12755): (WD repeat domain 3) This gene encodes a nuclear protein containing 10 WD repeats. WD repeats are approximately 30- to 40-amino acid domains containing several conserved residues, which usually include a trp-asp at the C-terminal end. Proteins belonging to the WD repeat family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPAG17 | NM_206996.4 | c.*170G>C | 3_prime_UTR_variant | 49/49 | ENST00000336338.10 | NP_996879.1 | ||
WDR3 | NM_006784.3 | c.2269-127C>G | intron_variant | ENST00000349139.6 | NP_006775.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPAG17 | ENST00000336338.10 | c.*170G>C | 3_prime_UTR_variant | 49/49 | 1 | NM_206996.4 | ENSP00000337804 | P1 | ||
WDR3 | ENST00000349139.6 | c.2269-127C>G | intron_variant | 1 | NM_006784.3 | ENSP00000308179 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0626 AC: 9517AN: 152026Hom.: 712 Cov.: 32
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GnomAD4 exome AF: 0.0265 AC: 16363AN: 618538Hom.: 746 Cov.: 9 AF XY: 0.0292 AC XY: 9422AN XY: 322774
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GnomAD4 genome AF: 0.0628 AC: 9561AN: 152144Hom.: 721 Cov.: 32 AF XY: 0.0633 AC XY: 4711AN XY: 74390
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at