5-76316507-T-G

Variant names:

• chr5-76316507-T-G
• rs2913257
• NM_014979.4:c.2001-8857T>G

Variant summary

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

The NM_014979.4(SV2C):​c.2001-8857T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.092 in 152,260 control chromosomes in the GnomAD database, including 705 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 0.092 (705 hom., cov: 32)
• Consequence: SV2C NM_014979.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SV2C	NM_014979.4	c.2001-8857T>G		intron_variant	Intron 12 of 12	ENST00000502798.7	NP_055794.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SV2C	ENST00000502798.7	c.2001-8857T>G		intron_variant	Intron 12 of 12	1	NM_014979.4	ENSP00000423541.2
SV2C	ENST00000322285.7	c.2000+14962T>G		intron_variant	Intron 12 of 12	2		ENSP00000316983.7

Frequencies

GnomAD3 genomes AF: 0.0920 AC: 13995 AN: 152142 Hom.: 701 Cov.: 32

Gnomad AFR AF: 0.0838

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0336

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0834

Gnomad OTH AF: 0.0936

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

GnomAD4 genome AF: 0.0920 AC: 14012 AN: 152260 Hom.: 705 Cov.: 32 AF XY: 0.0944 AC XY: 7028 AN XY: 74442

Gnomad4 AFR AF: 0.0839

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.0332

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.0833

Gnomad4 OTH AF: 0.0926

Alfa AF: 0.0766 Hom.: 299

Bravo AF: 0.0944

Asia WGS AF: 0.0800 AC: 276 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	3.0
DANN	Benign	0.26

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: rs2913257; hg19: chr5-75612332;