rs199577037
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_152415.3(VPS37A):āc.96G>Cā(p.Leu32=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000325 in 1,523,514 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. L32L) has been classified as Uncertain significance.
Frequency
Consequence
NM_152415.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS37A | NM_152415.3 | c.96G>C | p.Leu32= | synonymous_variant | 1/12 | ENST00000324849.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS37A | ENST00000324849.9 | c.96G>C | p.Leu32= | synonymous_variant | 1/12 | 1 | NM_152415.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000183 AC: 27AN: 147356Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000508 AC: 80AN: 157426Hom.: 0 AF XY: 0.000534 AC XY: 45AN XY: 84228
GnomAD4 exome AF: 0.000339 AC: 466AN: 1376056Hom.: 4 Cov.: 31 AF XY: 0.000348 AC XY: 236AN XY: 678692
GnomAD4 genome ? AF: 0.000197 AC: 29AN: 147458Hom.: 0 Cov.: 31 AF XY: 0.000265 AC XY: 19AN XY: 71672
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 53 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 03, 2023 | - - |
VPS37A-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 20, 2019 | 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