chr1-209965932-A-G
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001146262.4(SYT14):c.61+13176A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000594 in 454,224 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000073 ( 0 hom. )
Consequence
SYT14
NM_001146262.4 intron
NM_001146262.4 intron
Scores
13
Clinical Significance
Conservation
PhyloP100: -0.863
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 Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.027591199).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYT14 | NM_001146262.4 | c.61+13176A>G | intron_variant | ENST00000367019.6 | NP_001139734.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYT14 | ENST00000367019.6 | c.61+13176A>G | intron_variant | 1 | NM_001146262.4 | ENSP00000355986 |
Frequencies
GnomAD3 genomes AF: 0.0000331 AC: 5AN: 151020Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000463 AC: 6AN: 129706Hom.: 0 AF XY: 0.0000422 AC XY: 3AN XY: 71080
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GnomAD4 exome AF: 0.0000726 AC: 22AN: 303090Hom.: 0 Cov.: 0 AF XY: 0.000104 AC XY: 18AN XY: 172680
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GnomAD4 genome AF: 0.0000331 AC: 5AN: 151134Hom.: 0 Cov.: 31 AF XY: 0.0000542 AC XY: 4AN XY: 73744
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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 | Jan 08, 2021 | - - |
Computational scores
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Name
Calibrated prediction
Score
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BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N;N;N;N
PrimateAI
Benign
T
Sift4G
Benign
T
Vest4
MVP
ClinPred
T
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at