rs11960832

chr5-76219161-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014979.4(SV2C):c.913+9274C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,004 control chromosomes in the GnomAD database, including 15,891 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 0.42 (15891 hom., cov: 32)
• Consequence: SV2C NM_014979.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.929

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SV2C	NM_014979.4	c.913+9274C>T		intron_variant		ENST00000502798.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SV2C	ENST00000502798.7	c.913+9274C>T		intron_variant		1	NM_014979.4	P1
SV2C	ENST00000322285.7	c.913+9274C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64248 AN: 151886 Hom.: 15853 Cov.: 32

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.416

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.423 AC: 64335 AN: 152004 Hom.: 15891 Cov.: 32 AF XY: 0.420 AC XY: 31195 AN XY: 74298

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.414

Alfa AF: 0.342 Hom.: 9907

Bravo AF: 0.446

Asia WGS AF: 0.339 AC: 1180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.38
Dann	Benign	0.32

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

Other links and lift over

dbSNP: rs11960832; hg19: chr5-75514986;