chr1-12244266-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015378.4(VPS13D):c.196C>T(p.Leu66Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000366 in 1,613,174 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_015378.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VPS13D | ENST00000620676.6 | c.196C>T | p.Leu66Phe | missense_variant | Exon 4 of 70 | 1 | NM_015378.4 | ENSP00000478104.1 | ||
VPS13D | ENST00000613099.4 | c.196C>T | p.Leu66Phe | missense_variant | Exon 4 of 69 | 1 | ENSP00000482233.1 | |||
VPS13D | ENST00000476169.1 | n.-158C>T | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250408Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135338
GnomAD4 exome AF: 0.0000370 AC: 54AN: 1460978Hom.: 0 Cov.: 31 AF XY: 0.0000440 AC XY: 32AN XY: 726780
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74352
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.196C>T (p.L66F) alteration is located in exon 4 (coding exon 3) of the VPS13D gene. This alteration results from a C to T substitution at nucleotide position 196, causing the leucine (L) at amino acid position 66 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
See cases Uncertain:1
ACMG categories: PM2,BP4 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at