12-108937386-C-A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_018711.5(SVOP):​c.898-49G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)

Consequence

SVOP
NM_018711.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.456

Publications

11 publications found
Variant links:
Genes affected
SVOP (HGNC:25417): (SV2 related protein) Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be located in synaptic vesicle. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SVOPNM_018711.5 linkc.898-49G>T intron_variant Intron 9 of 15 ENST00000610966.5 NP_061181.1 Q8N4V2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SVOPENST00000610966.5 linkc.898-49G>T intron_variant Intron 9 of 15 1 NM_018711.5 ENSP00000479104.1 Q8N4V2
SVOPENST00000551211.1 linkn.63-49G>T intron_variant Intron 1 of 1 3

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
24
GnomAD4 genome
Cov.:
31
Alfa
AF:
0.00
Hom.:
58296

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.013
DANN
Benign
0.38
PhyloP100
-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

Other links and lift over

dbSNP: rs3918305; hg19: chr12-109331162; API