5-75998585-C-T

Position:

• chr5-75998585-C-T

Variant summary

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

The XM_011543282.4(SV2C):​c.-101-133065C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 152,108 control chromosomes in the GnomAD database, including 51,647 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 0.82 (51647 hom., cov: 31)
• Consequence: SV2C XM_011543282.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SV2C	XM_011543282.4	c.-101-133065C>T		intron_variant			XP_011541584.2
		n.75998585C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.822 AC: 124944 AN: 151990 Hom.: 51593 Cov.: 31

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.852

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

GnomAD4 genome AF: 0.822 AC: 125049 AN: 152108 Hom.: 51647 Cov.: 31 AF XY: 0.819 AC XY: 60870 AN XY: 74350

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.803

Gnomad4 ASJ AF: 0.804

Gnomad4 EAS AF: 0.742

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.847

Alfa AF: 0.798 Hom.: 80726

Bravo AF: 0.827

Asia WGS AF: 0.749 AC: 2608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.93
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10214163; hg19: chr5-75294410;