rs7279487
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_203446.3(SYNJ1):c.*2291A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,706 control chromosomes in the GnomAD database, including 1,290 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 0.13 ( 1287 hom., cov: 33)
Exomes 𝑓: 0.12 ( 3 hom. )
Consequence
SYNJ1
NM_203446.3 3_prime_UTR
NM_203446.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.896
Genes affected
SYNJ1 (HGNC:11503): (synaptojanin 1) This gene encodes a phosphoinositide phosphatase that regulates levels of membrane phosphatidylinositol-4,5-bisphosphate. As such, expression of this enzyme may affect synaptic transmission and membrane trafficking. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYNJ1 | NM_203446.3 | c.*2291A>G | 3_prime_UTR_variant | 33/33 | ENST00000674351.1 | NP_982271.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYNJ1 | ENST00000674351.1 | c.*2291A>G | 3_prime_UTR_variant | 33/33 | NM_203446.3 | ENSP00000501530 |
Frequencies
GnomAD3 genomes AF: 0.127 AC: 19271AN: 152156Hom.: 1286 Cov.: 33
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GnomAD4 exome AF: 0.120 AC: 52AN: 432Hom.: 3 Cov.: 0 AF XY: 0.142 AC XY: 37AN XY: 260
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GnomAD4 genome AF: 0.127 AC: 19288AN: 152274Hom.: 1287 Cov.: 33 AF XY: 0.123 AC XY: 9186AN XY: 74472
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at