3-49642354-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BS1BS2
The NM_003458.4(BSN):c.720G>A(p.Gln240=) variant causes a synonymous change. The variant allele was found at a frequency of 0.000555 in 1,599,194 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.00023 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00059 ( 22 hom. )
Consequence
BSN
NM_003458.4 synonymous
NM_003458.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.75
Genes affected
BSN (HGNC:1117): (bassoon presynaptic cytomatrix protein) Neurotransmitters are released from a specific site in the axon terminal called the active zone, which is composed of synaptic vesicles and a meshwork of cytoskeleton underlying the plasma membrane. The protein encoded by this gene is thought to be a scaffolding protein involved in organizing the presynaptic cytoskeleton. The gene is expressed primarily in neurons in the brain. A similar gene product in rodents is concentrated in the active zone of axon terminals and tightly associated with cytoskeletal structures, and is essential for regulating neurotransmitter release from a subset of synapses. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
Variant 3-49642354-G-A is Benign according to our data. Variant chr3-49642354-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3040984.Status of the report is no_assertion_criteria_provided, 0 stars.
BS1
Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.00059 (853/1446856) while in subpopulation EAS AF= 0.0216 (848/39174). AF 95% confidence interval is 0.0204. There are 22 homozygotes in gnomad4_exome. There are 432 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 35 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BSN | NM_003458.4 | c.720G>A | p.Gln240= | synonymous_variant | 3/12 | ENST00000296452.5 | NP_003449.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BSN | ENST00000296452.5 | c.720G>A | p.Gln240= | synonymous_variant | 3/12 | 1 | NM_003458.4 | ENSP00000296452 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152220Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000108 AC: 24AN: 222996Hom.: 0 AF XY: 0.0000996 AC XY: 12AN XY: 120430
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GnomAD4 exome AF: 0.000590 AC: 853AN: 1446856Hom.: 22 Cov.: 32 AF XY: 0.000601 AC XY: 432AN XY: 718636
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GnomAD4 genome AF: 0.000230 AC: 35AN: 152338Hom.: 0 Cov.: 33 AF XY: 0.000295 AC XY: 22AN XY: 74502
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
BSN-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 26, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational 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