rs775846620
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Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_001146262.4(SYT14):βc.198_203delβ(p.Ser66_Thr67del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000241 in 1,612,690 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (β ).
Frequency
Genomes: π 0.000085 ( 0 hom., cov: 32)
Exomes π: 0.00026 ( 0 hom. )
Consequence
SYT14
NM_001146262.4 inframe_deletion
NM_001146262.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.37
Genes affected
SYT14 (HGNC:23143): (synaptotagmin 14) This gene is a member of the synaptotagmin gene family and encodes a protein similar to other family members that mediate membrane trafficking in synaptic transmission. The encoded protein is a calcium-independent synaptotagmin. Mutations in this gene are a cause of autosomal recessive spinocerebellar ataxia-11 (SCAR11), and a t(1;3) translocation of this gene has been associated with neurodevelopmental abnormalities. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 4. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Nonframeshift variant in NON repetitive region in NM_001146262.4.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYT14 | NM_001146262.4 | c.198_203del | p.Ser66_Thr67del | inframe_deletion | 3/9 | ENST00000367019.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYT14 | ENST00000367019.6 | c.198_203del | p.Ser66_Thr67del | inframe_deletion | 3/9 | 1 | NM_001146262.4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000855 AC: 13AN: 152074Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000679 AC: 17AN: 250538Hom.: 0 AF XY: 0.0000664 AC XY: 9AN XY: 135592
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GnomAD4 exome AF: 0.000257 AC: 375AN: 1460616Hom.: 0 AF XY: 0.000235 AC XY: 171AN XY: 726536
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GnomAD4 genome ? AF: 0.0000855 AC: 13AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74282
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 24, 2021 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at