chr20-1308322-G-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001318234.2(SNPH):c.*2268G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 152,442 control chromosomes in the GnomAD database, including 17,360 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 0.47 ( 17337 hom., cov: 33)
Exomes 𝑓: 0.37 ( 23 hom. )
Consequence
SNPH
NM_001318234.2 3_prime_UTR
NM_001318234.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.162
Genes affected
SNPH (HGNC:15931): (syntaphilin) Syntaxin-1, synaptobrevin/VAMP, and SNAP25 interact to form the SNARE complex, which is required for synaptic vesicle docking and fusion. The protein encoded by this gene is membrane-associated and inhibits SNARE complex formation by binding free syntaxin-1. Expression of this gene appears to be brain-specific. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
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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=-0.83).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNPH | NM_001318234.2 | c.*2268G>A | 3_prime_UTR_variant | 7/7 | ENST00000381867.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNPH | ENST00000381867.6 | c.*2268G>A | 3_prime_UTR_variant | 7/7 | 1 | NM_001318234.2 | P3 | ||
SNPH | ENST00000381873.7 | c.*2268G>A | 3_prime_UTR_variant | 6/6 | 1 | A1 | |||
SNPH | ENST00000614659.1 | c.*2268G>A | 3_prime_UTR_variant | 4/4 | 1 | P3 |
Frequencies
GnomAD3 genomes AF: 0.466 AC: 70865AN: 152012Hom.: 17316 Cov.: 33
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GnomAD4 exome AF: 0.372 AC: 116AN: 312Hom.: 23 Cov.: 0 AF XY: 0.376 AC XY: 88AN XY: 234
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GnomAD4 genome AF: 0.466 AC: 70924AN: 152130Hom.: 17337 Cov.: 33 AF XY: 0.455 AC XY: 33841AN XY: 74360
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ClinVar
Not reported inComputational 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