5-75998585-C-T

Variant names:

• chr5-75998585-C-T
• rs10214163
• XM_011543282.4:c.-101-133065C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SV2C	XM_011543282.4	c.-101-133065C>T		intron_variant	Intron 1 of 12		XP_011541584.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.899 AC: 37337 AN: 41530

American (AMR) AF: 0.803 AC: 12254 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 2792 AN: 3472

East Asian (EAS) AF: 0.742 AC: 3826 AN: 5158

South Asian (SAS) AF: 0.728 AC: 3503 AN: 4810

European-Finnish (FIN) AF: 0.816 AC: 8641 AN: 10584

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53910 AN: 67968

Other (OTH) AF: 0.847 AC: 1790 AN: 2114

Alfa AF: 0.801 Hom.: 184699

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
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs10214163; hg19: chr5-75294410;