chr9-77371141-A-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_033305.3(VPS13A):c.9069A>T(p.Gly3023=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,613,716 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G3023G) has been classified as Benign.
Frequency
Consequence
NM_033305.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS13A | NM_033305.3 | c.9069A>T | p.Gly3023= | synonymous_variant | 67/72 | ENST00000360280.8 | |
VPS13A | NM_001018037.2 | c.8952A>T | p.Gly2984= | synonymous_variant | 66/71 | ||
VPS13A | NM_015186.4 | c.9069A>T | p.Gly3023= | synonymous_variant | 67/69 | ||
VPS13A | NM_001018038.3 | c.9069A>T | p.Gly3023= | synonymous_variant | 67/69 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS13A | ENST00000360280.8 | c.9069A>T | p.Gly3023= | synonymous_variant | 67/72 | 1 | NM_033305.3 | P4 | |
VPS13A | ENST00000376636.7 | c.8952A>T | p.Gly2984= | synonymous_variant | 66/71 | 1 | |||
VPS13A | ENST00000643348.1 | c.9069A>T | p.Gly3023= | synonymous_variant | 67/69 | ||||
VPS13A | ENST00000645632.1 | c.9069A>T | p.Gly3023= | synonymous_variant | 67/69 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152008Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250736Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135560
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461708Hom.: 0 Cov.: 55 AF XY: 0.0000179 AC XY: 13AN XY: 727150
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152008Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74232
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at