chr5-76081726-G-T

Position:

• chr5-76081726-G-T

Variant summary

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

The XM_011543282.4(SV2C):​c.-101-49924G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 152,004 control chromosomes in the GnomAD database, including 25,925 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 0.57 (25925 hom., cov: 32)
• Consequence: SV2C XM_011543282.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400

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-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SV2C	XM_011543282.4	c.-101-49924G>T		intron_variant			XP_011541584.2
SV2C-AS1	NR_183290.1	n.1170C>A		non_coding_transcript_exon_variant	2/2
		n.76081726G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85974 AN: 151886 Hom.: 25881 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.566 AC: 86077 AN: 152004 Hom.: 25925 Cov.: 32 AF XY: 0.569 AC XY: 42269 AN XY: 74296

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.533

Alfa AF: 0.514 Hom.: 7341

Bravo AF: 0.582

Asia WGS AF: 0.706 AC: 2453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs30196; hg19: chr5-75377551;