rs10514058

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.321
Variant links:
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]

Genome browser will be placed here

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
SV2CNM_014979.4 linkuse as main transcriptc.-101-4789G>A intron_variant ENST00000502798.7 NP_055794.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SV2CENST00000502798.7 linkuse as main transcriptc.-101-4789G>A intron_variant 1 NM_014979.4 ENSP00000423541 P1
SV2CENST00000322285.7 linkuse as main transcriptc.-101-4789G>A intron_variant 2 ENSP00000316983

Frequencies

GnomAD3 genomes
AF:
0.0202
AC:
3075
AN:
152128
Hom.:
47
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00422
Gnomad AMI
AF:
0.0307
Gnomad AMR
AF:
0.0156
Gnomad ASJ
AF:
0.0870
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.0450
Gnomad FIN
AF:
0.0157
Gnomad MID
AF:
0.0443
Gnomad NFE
AF:
0.0277
Gnomad OTH
AF:
0.0229
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0201
AC:
3067
AN:
152244
Hom.:
46
Cov.:
32
AF XY:
0.0204
AC XY:
1516
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.00421
Gnomad4 AMR
AF:
0.0156
Gnomad4 ASJ
AF:
0.0870
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.0440
Gnomad4 FIN
AF:
0.0157
Gnomad4 NFE
AF:
0.0277
Gnomad4 OTH
AF:
0.0222
Alfa
AF:
0.00961
Hom.:
4
Bravo
AF:
0.0183
Asia WGS
AF:
0.0250
AC:
86
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
2.4
DANN
Benign
0.55

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10514058; hg19: chr5-75422686; API