chr1-12244235-TCTC-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_015378.4(VPS13D):c.176-8_176-6del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000206 in 1,599,958 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_015378.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS13D | NM_015378.4 | c.176-8_176-6del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000620676.6 | |||
VPS13D | NM_018156.4 | c.176-8_176-6del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS13D | ENST00000620676.6 | c.176-8_176-6del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_015378.4 | P3 | |||
VPS13D | ENST00000613099.4 | c.176-8_176-6del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000210 AC: 5AN: 238394Hom.: 0 AF XY: 0.0000232 AC XY: 3AN XY: 129062
GnomAD4 exome AF: 0.0000166 AC: 24AN: 1447624Hom.: 0 AF XY: 0.0000167 AC XY: 12AN XY: 719706
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152334Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74488
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 21, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at