12-101729122-AT-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP5BS2_Supporting
The NM_001177949.2(SYCP3):c.643del(p.Ile215LeufsTer2) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000696 in 1,594,494 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: 𝑓 0.000040 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000073 ( 0 hom. )
Consequence
SYCP3
NM_001177949.2 frameshift
NM_001177949.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.782
Genes affected
SYCP3 (HGNC:18130): (synaptonemal complex protein 3) This gene encodes an essential structural component of the synaptonemal complex. This complex is involved in synapsis, recombination and segregation of meiotic chromosomes. Mutations in this gene are associated with azoospermia in males and susceptibility to pregnancy loss in females. Alternate splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, May 2010]
CHPT1 (HGNC:17852): (choline phosphotransferase 1) Enables diacylglycerol cholinephosphotransferase activity. Involved in phosphatidylcholine biosynthetic process and platelet activating factor biosynthetic process. Predicted to be located in Golgi membrane. Predicted to be active in Golgi apparatus and endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PP5
Variant 12-101729122-AT-A is Pathogenic according to our data. Variant chr12-101729122-AT-A is described in ClinVar as [Pathogenic]. Clinvar id is 5371.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High AC in GnomAd4 at 6 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYCP3 | NM_001177949.2 | c.643del | p.Ile215LeufsTer2 | frameshift_variant | 8/9 | ENST00000392924.2 | |
CHPT1 | NM_020244.3 | downstream_gene_variant | ENST00000229266.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYCP3 | ENST00000392924.2 | c.643del | p.Ile215LeufsTer2 | frameshift_variant | 8/9 | 1 | NM_001177949.2 | P1 | |
CHPT1 | ENST00000229266.8 | downstream_gene_variant | 1 | NM_020244.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000397 AC: 6AN: 151136Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000727 AC: 105AN: 1443358Hom.: 0 Cov.: 30 AF XY: 0.0000793 AC XY: 57AN XY: 718392
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GnomAD4 genome AF: 0.0000397 AC: 6AN: 151136Hom.: 0 Cov.: 32 AF XY: 0.0000407 AC XY: 3AN XY: 73750
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Spermatogenic failure 4 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 22, 2003 | - - |
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at