5-76209850-C-T
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_014979.4(SV2C):c.876C>T(p.Tyr292=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000258 in 1,614,134 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00018 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00027 ( 1 hom. )
Consequence
SV2C
NM_014979.4 synonymous
NM_014979.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.382
Genes affected
SV2C (HGNC:30670): (synaptic vesicle glycoprotein 2C) Predicted to enable transmembrane transporter activity. Predicted to be involved in chemical synaptic transmission; neurotransmitter transport; and transmembrane transport. Predicted to be located in plasma membrane and synaptic vesicle. Predicted to be active in neuron projection and synaptic vesicle membrane. Predicted to be integral component of synaptic vesicle membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
Variant 5-76209850-C-T is Benign according to our data. Variant chr5-76209850-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3048043.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.382 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SV2C | NM_014979.4 | c.876C>T | p.Tyr292= | synonymous_variant | 4/13 | ENST00000502798.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SV2C | ENST00000502798.7 | c.876C>T | p.Tyr292= | synonymous_variant | 4/13 | 1 | NM_014979.4 | P1 | |
SV2C | ENST00000322285.7 | c.876C>T | p.Tyr292= | synonymous_variant | 4/13 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000177 AC: 27AN: 152238Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000563 AC: 141AN: 250334Hom.: 0 AF XY: 0.000686 AC XY: 93AN XY: 135530
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GnomAD4 exome AF: 0.000267 AC: 390AN: 1461778Hom.: 1 Cov.: 31 AF XY: 0.000341 AC XY: 248AN XY: 727168
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GnomAD4 genome AF: 0.000177 AC: 27AN: 152356Hom.: 0 Cov.: 33 AF XY: 0.000268 AC XY: 20AN XY: 74512
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SV2C-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 08, 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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at