5-76225103-T-G

Variant names:

• chr5-76225103-T-G
• rs981113
• NM_014979.4:c.913+15216T>G

Variant summary

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

The NM_014979.4(SV2C):​c.913+15216T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 152,062 control chromosomes in the GnomAD database, including 29,420 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 0.61 (29420 hom., cov: 31)
• Consequence: SV2C NM_014979.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SV2C	NM_014979.4	c.913+15216T>G		intron_variant	Intron 4 of 12	ENST00000502798.7	NP_055794.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SV2C	ENST00000502798.7	c.913+15216T>G		intron_variant	Intron 4 of 12	1	NM_014979.4	ENSP00000423541.2
SV2C	ENST00000322285.7	c.913+15216T>G		intron_variant	Intron 4 of 12	2		ENSP00000316983.7

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93228 AN: 151944 Hom.: 29392 Cov.: 31

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.614 AC: 93312 AN: 152062 Hom.: 29420 Cov.: 31 AF XY: 0.605 AC XY: 44972 AN XY: 74322

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.614

Alfa AF: 0.588 Hom.: 36037

Bravo AF: 0.638

Asia WGS AF: 0.453 AC: 1576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.43
DANN	Benign	0.46

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: rs981113; hg19: chr5-75520928;