12-101729443-C-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001177949.2(SYCP3):c.553-230G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 427,128 control chromosomes in the GnomAD database, including 76,712 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.62 ( 30016 hom., cov: 32)
Exomes 𝑓: 0.57 ( 46696 hom. )
Consequence
SYCP3
NM_001177949.2 intron
NM_001177949.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.954
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 Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP6
Variant 12-101729443-C-A is Benign according to our data. Variant chr12-101729443-C-A is described in ClinVar as [Benign]. Clinvar id is 1229163.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYCP3 | NM_001177949.2 | c.553-230G>T | intron_variant | ENST00000392924.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYCP3 | ENST00000392924.2 | c.553-230G>T | intron_variant | 1 | NM_001177949.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.618 AC: 93796AN: 151834Hom.: 29971 Cov.: 32
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GnomAD4 exome AF: 0.572 AC: 157534AN: 275178Hom.: 46696 Cov.: 4 AF XY: 0.574 AC XY: 83833AN XY: 146036
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GnomAD4 genome AF: 0.618 AC: 93906AN: 151950Hom.: 30016 Cov.: 32 AF XY: 0.621 AC XY: 46140AN XY: 74272
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ClinVar
Significance: Benign
Submissions summary: Benign:2
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 | Nov 12, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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