dbSNP rs3733860: SV2C:c.*1442C>A (chr5-76326989-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014979.4(SV2C):c.*1442C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,084 control chromosomes in the GnomAD database, including 1,765 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 0.12 ( 1765 hom., cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SV2C
NM_014979.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0360

Publications

11 publications found

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:

SV2C-AS2 (HGNC:58251):

SV2C-AS2 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_014979.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014979.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SV2C	NM_014979.4	MANE Select	c.*1442C>A		3_prime_UTR	Exon 13 of 13	NP_055794.3	Q496J9
	SV2C	NM_001297716.2		c.2000+25444C>A		intron	N/A	NP_001284645.1	B3KT41

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SV2C	ENST00000502798.7	TSL:1 MANE Select	c.*1442C>A	3_prime_UTR	Exon 13 of 13	ENSP00000423541.2	Q496J9
SV2C	ENST00000322285.7	TSL:2	c.2000+25444C>A	intron	N/A	ENSP00000316983.7	B3KT41
SV2C-AS2	ENST00000502589.2	TSL:5	n.531+9332G>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.125

AC:

18963

AN:

151964

Hom.:

1764

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0328

Gnomad AMI

AF:

0.0877

Gnomad AMR

AF:

0.221

Gnomad ASJ

AF:

0.0980

Gnomad EAS

AF:

0.419

Gnomad SAS

AF:

0.125

Gnomad FIN

AF:

0.126

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.139

Gnomad OTH

AF:

0.128

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

GnomAD4 genome

AF:

0.125

AC:

18966

AN:

152084

Hom.:

1765

Cov.:

AF XY:

0.125

AC XY:

9315

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.0327

AC:

1356

AN:

41484

American (AMR)

AF:

0.221

AC:

3383

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0980

AC:

340

AN:

3468

East Asian (EAS)

AF:

0.419

AC:

2153

AN:

5142

South Asian (SAS)

AF:

0.125

AC:

601

AN:

4812

European-Finnish (FIN)

AF:

0.126

AC:

1334

AN:

10574

Middle Eastern (MID)

AF:

0.0850

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.139

AC:

9425

AN:

67998

Other (OTH)

AF:

0.127

AC:

269

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

814

1629

2443

3258

4072

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

208

416

624

832

1040

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.129

Hom.:

2870

Bravo

AF:

0.130

Asia WGS

AF:

0.243

AC:

846

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

(source)

DANN

Benign

0.73

PhyloP100

0.036

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over