rs10514058
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000502798.7(SV2C):c.-101-4789G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0201 in 152,244 control chromosomes in the GnomAD database, including 46 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 0.020 ( 46 hom., cov: 32)
Consequence
SV2C
ENST00000502798.7 intron
ENST00000502798.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.321
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 Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0201 (3067/152244) while in subpopulation SAS AF= 0.044 (212/4814). AF 95% confidence interval is 0.0392. There are 46 homozygotes in gnomad4. There are 1516 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 46 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SV2C | NM_014979.4 | c.-101-4789G>A | intron_variant | ENST00000502798.7 | NP_055794.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SV2C | ENST00000502798.7 | c.-101-4789G>A | intron_variant | 1 | NM_014979.4 | ENSP00000423541 | P1 | |||
SV2C | ENST00000322285.7 | c.-101-4789G>A | intron_variant | 2 | ENSP00000316983 |
Frequencies
GnomAD3 genomes AF: 0.0202 AC: 3075AN: 152128Hom.: 47 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0201 AC: 3067AN: 152244Hom.: 46 Cov.: 32 AF XY: 0.0204 AC XY: 1516AN XY: 74438
GnomAD4 genome
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86
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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