Genetic Variant SV2C:p.Arg120Arg (chr5-76132110-G-A) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_014979.4(SV2C):c.360G>A(p.Arg120Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 1,613,672 control chromosomes in the GnomAD database, including 417,424 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.59 ( 29420 hom., cov: 31)

Exomes 𝑓: 0.72 ( 388004 hom. )

Consequence

SV2C
NM_014979.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -4.26

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]

SV2C links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 5-76132110-G-A is Benign according to our data. Variant chr5-76132110-G-A is described in ClinVar as [Benign]. Clinvar id is 3060767.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-4.26 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SV2C	NM_014979.4 link	c.360G>A	p.Arg120Arg	synonymous_variant	Exon 2 of 13	ENST00000502798.7	NP_055794.3	Q496J9B3KT41

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SV2C	ENST00000502798.7 link	c.360G>A	p.Arg120Arg	synonymous_variant	Exon 2 of 13	1	NM_014979.4	ENSP00000423541.2		Q496J9
SV2C	ENST00000322285.7 link	c.360G>A	p.Arg120Arg	synonymous_variant	Exon 2 of 13	2		ENSP00000316983.7		B3KT41

Frequencies

GnomAD3 genomes

AF:

0.591

AC:

89760

AN:

151872

Hom.:

29417

Cov.:

show subpopulations

Gnomad AFR

AF:

0.330

Gnomad AMI

AF:

0.762

Gnomad AMR

AF:

0.502

Gnomad ASJ

AF:

0.747

Gnomad EAS

AF:

0.336

Gnomad SAS

AF:

0.657

Gnomad FIN

AF:

0.677

Gnomad MID

AF:

0.665

Gnomad NFE

AF:

0.760

Gnomad OTH

AF:

0.597

GnomAD3 exomes

AF:

0.626

AC:

155839

AN:

248990

Hom.:

52687

AF XY:

0.645

AC XY:

87076

AN XY:

135072

show subpopulations

Gnomad AFR exome

AF:

0.316

Gnomad AMR exome

AF:

0.388

Gnomad ASJ exome

AF:

0.736

Gnomad EAS exome

AF:

0.329

Gnomad SAS exome

AF:

0.663

Gnomad FIN exome

AF:

0.686

Gnomad NFE exome

AF:

0.754

Gnomad OTH exome

AF:

0.676

GnomAD4 exome

AF:

0.719

AC:

1051093

AN:

1461682

Hom.:

388004

Cov.:

AF XY:

0.720

AC XY:

523693

AN XY:

727120

show subpopulations

Gnomad4 AFR exome

AF:

0.309

Gnomad4 AMR exome

AF:

0.405

Gnomad4 ASJ exome

AF:

0.739

Gnomad4 EAS exome

AF:

0.346

Gnomad4 SAS exome

AF:

0.665

Gnomad4 FIN exome

AF:

0.696

Gnomad4 NFE exome

AF:

0.765

Gnomad4 OTH exome

AF:

0.681

GnomAD4 genome

AF:

0.591

AC:

89781

AN:

151990

Hom.:

29420

Cov.:

AF XY:

0.585

AC XY:

43425

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.330

Gnomad4 AMR

AF:

0.502

Gnomad4 ASJ

AF:

0.747

Gnomad4 EAS

AF:

0.335

Gnomad4 SAS

AF:

0.658

Gnomad4 FIN

AF:

0.677

Gnomad4 NFE

AF:

0.760

Gnomad4 OTH

AF:

0.600

Alfa

AF:

0.715

Hom.:

52477

Bravo

AF:

0.558

Asia WGS

AF:

0.490

AC:

1706

AN:

3476

EpiCase

AF:

0.745

EpiControl

AF:

0.753

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

SV2C-related disorder

Benign:1

Oct 16, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.43

DANN

Benign

0.67

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over