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GeneBe

5-76132245-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_014979.4(SV2C):c.495C>T(p.Asp165=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00242 in 1,613,976 control chromosomes in the GnomAD database, including 64 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.012 ( 32 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 32 hom. )

Consequence

SV2C
NM_014979.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.486
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 -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 5-76132245-C-T is Benign according to our data. Variant chr5-76132245-C-T is described in ClinVar as [Benign]. Clinvar id is 777396.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.486 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.012 (1829/152132) while in subpopulation AFR AF= 0.0413 (1712/41498). AF 95% confidence interval is 0.0396. There are 32 homozygotes in gnomad4. There are 863 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 32 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SV2CNM_014979.4 linkuse as main transcriptc.495C>T p.Asp165= synonymous_variant 2/13 ENST00000502798.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SV2CENST00000502798.7 linkuse as main transcriptc.495C>T p.Asp165= synonymous_variant 2/131 NM_014979.4 P1
SV2CENST00000322285.7 linkuse as main transcriptc.495C>T p.Asp165= synonymous_variant 2/132

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0120
AC:
1825
AN:
152014
Hom.:
32
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0413
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00452
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00406
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000162
Gnomad OTH
AF:
0.00765
GnomAD3 exomes
AF:
0.00332
AC:
827
AN:
249456
Hom.:
13
AF XY:
0.00239
AC XY:
324
AN XY:
135320
show subpopulations
Gnomad AFR exome
AF:
0.0418
Gnomad AMR exome
AF:
0.00194
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00378
Gnomad SAS exome
AF:
0.0000980
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000239
Gnomad OTH exome
AF:
0.00231
GnomAD4 exome
AF:
0.00142
AC:
2081
AN:
1461844
Hom.:
32
Cov.:
34
AF XY:
0.00121
AC XY:
878
AN XY:
727212
show subpopulations
Gnomad4 AFR exome
AF:
0.0433
Gnomad4 AMR exome
AF:
0.00230
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00247
Gnomad4 SAS exome
AF:
0.000104
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000156
Gnomad4 OTH exome
AF:
0.00376
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0120
AC:
1829
AN:
152132
Hom.:
32
Cov.:
32
AF XY:
0.0116
AC XY:
863
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.0413
Gnomad4 AMR
AF:
0.00452
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00407
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000162
Gnomad4 OTH
AF:
0.00757
Alfa
AF:
0.00559
Hom.:
4
Bravo
AF:
0.0143
Asia WGS
AF:
0.00491
AC:
18
AN:
3478
EpiCase
AF:
0.000109
EpiControl
AF:
0.000237

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 submitterclinical testingInvitaeApr 24, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.49
Cadd
Benign
0.78
Dann
Benign
0.54

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: rs73130289; hg19: chr5-75428070; API