chr5-76081726-G-T

Variant names:

• chr5-76081726-G-T
• rs30196
• ENST00000503652.2:n.911C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000503652.2(SV2C-AS1):​n.911C>A variant causes a non coding transcript exon 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-AS1 ENST00000503652.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 7 publications found

Genes affected

SV2C-AS1 (HGNC:55583): (SV2C antisense RNA 1)

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503652.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SV2C-AS1	NR_183290.1		n.1170C>A		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SV2C-AS1	ENST00000503652.2	TSL:3	n.911C>A		non_coding_transcript_exon	Exon 2 of 2
	SV2C-AS1	ENST00000826264.1		n.1026C>A		non_coding_transcript_exon	Exon 2 of 2
	SV2C-AS1	ENST00000826265.1		n.782C>A		non_coding_transcript_exon	Exon 2 of 2

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

African (AFR) AF: 0.770 AC: 31919 AN: 41450

American (AMR) AF: 0.548 AC: 8378 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1774 AN: 3468

East Asian (EAS) AF: 0.729 AC: 3755 AN: 5150

South Asian (SAS) AF: 0.671 AC: 3230 AN: 4814

European-Finnish (FIN) AF: 0.419 AC: 4425 AN: 10558

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30833 AN: 67972

Other (OTH) AF: 0.533 AC: 1121 AN: 2102

Alfa AF: 0.516 Hom.: 9107

Bravo AF: 0.582

Asia WGS AF: 0.706 AC: 2453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.67
PhyloP100		0.040

Splicing

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

Other links and lift over

dbSNP: rs30196; hg19: chr5-75377551;