chr6-83582313-A-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001242792.2(SNAP91):c.2058T>G(p.Thr686=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00147 in 1,613,702 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0082 ( 14 hom., cov: 32)
Exomes 𝑓: 0.00077 ( 9 hom. )
Consequence
SNAP91
NM_001242792.2 synonymous
NM_001242792.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.82
Genes affected
SNAP91 (HGNC:14986): (synaptosome associated protein 91) Predicted to enable several functions, including SNARE binding activity; clathrin binding activity; and phosphatidylinositol binding activity. Acts upstream of or within regulation of clathrin-dependent endocytosis. Predicted to be located in several cellular components, including postsynaptic density; presynaptic endosome; and presynaptic membrane. Predicted to be extrinsic component of endosome membrane. Predicted to be active in several cellular components, including Schaffer collateral - CA1 synapse; cytoplasmic vesicle; and parallel fiber to Purkinje cell synapse. Predicted to be extrinsic component of presynaptic endocytic zone membrane. Biomarker of Alzheimer's disease. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
?
Variant 6-83582313-A-C is Benign according to our data. Variant chr6-83582313-A-C is described in ClinVar as [Benign]. Clinvar id is 787305.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.82 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00822 (1251/152226) while in subpopulation AFR AF= 0.0284 (1181/41530). AF 95% confidence interval is 0.0271. There are 14 homozygotes in gnomad4. There are 595 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 14 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNAP91 | NM_001242792.2 | c.2058T>G | p.Thr686= | synonymous_variant | 23/30 | ENST00000369694.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNAP91 | ENST00000369694.7 | c.2058T>G | p.Thr686= | synonymous_variant | 23/30 | 5 | NM_001242792.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00822 AC: 1250AN: 152108Hom.: 14 Cov.: 32
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GnomAD3 exomes AF: 0.00218 AC: 542AN: 248876Hom.: 5 AF XY: 0.00167 AC XY: 226AN XY: 135014
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GnomAD4 exome AF: 0.000770 AC: 1125AN: 1461476Hom.: 9 Cov.: 31 AF XY: 0.000659 AC XY: 479AN XY: 727006
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GnomAD4 genome ? AF: 0.00822 AC: 1251AN: 152226Hom.: 14 Cov.: 32 AF XY: 0.00799 AC XY: 595AN XY: 74430
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 04, 2017 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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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