1-12242583-C-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 2P and 15B. PM2BP4_ModerateBP6_Very_StrongBP7BS1
The NM_015378.4(VPS13D):c.168C>G(p.Val56Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000711 in 1,613,750 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_015378.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VPS13D | ENST00000620676.6 | c.168C>G | p.Val56Val | synonymous_variant | Exon 3 of 70 | 1 | NM_015378.4 | ENSP00000478104.1 | ||
VPS13D | ENST00000613099.4 | c.168C>G | p.Val56Val | synonymous_variant | Exon 3 of 69 | 1 | ENSP00000482233.1 |
Frequencies
GnomAD3 genomes AF: 0.000355 AC: 54AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000211 AC: 53AN: 251292Hom.: 0 AF XY: 0.000213 AC XY: 29AN XY: 135850
GnomAD4 exome AF: 0.000748 AC: 1093AN: 1461586Hom.: 0 Cov.: 30 AF XY: 0.000717 AC XY: 521AN XY: 727078
GnomAD4 genome AF: 0.000355 AC: 54AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74334
ClinVar
Submissions by phenotype
not provided Benign:2
VPS13D: BP4, BP7 -
- -
VPS13D-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at