rs724307
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_016524.4(SYT17):c.1229-12221C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 151,978 control chromosomes in the GnomAD database, including 21,833 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 0.52 ( 21833 hom., cov: 32)
Consequence
SYT17
NM_016524.4 intron
NM_016524.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.16
Genes affected
SYT17 (HGNC:24119): (synaptotagmin 17) Predicted to enable several functions, including calcium ion binding activity; phospholipid binding activity; and syntaxin binding activity. Involved in positive regulation of dendrite extension. Predicted to be located in trans-Golgi network. Predicted to be active in exocytic vesicle and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.88).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYT17 | NM_016524.4 | c.1229-12221C>A | intron_variant | ENST00000355377.7 | |||
LOC105371114 | XR_001752097.2 | n.724G>T | non_coding_transcript_exon_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYT17 | ENST00000355377.7 | c.1229-12221C>A | intron_variant | 1 | NM_016524.4 | P1 | |||
SYT17 | ENST00000562034.5 | c.1046-12221C>A | intron_variant | 1 | |||||
SYT17 | ENST00000562711.6 | c.1217-12221C>A | intron_variant | 2 | |||||
SYT17 | ENST00000568433.1 | c.311-12221C>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.519 AC: 78882AN: 151860Hom.: 21840 Cov.: 32
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.519 AC: 78895AN: 151978Hom.: 21833 Cov.: 32 AF XY: 0.522 AC XY: 38772AN XY: 74286
GnomAD4 genome
?
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151978
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32
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38772
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74286
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2132
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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