chr9-77321541-A-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_033305.3(VPS13A):āc.5625A>Gā(p.Leu1875=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00112 in 1,613,544 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. L1875L) has been classified as Likely benign.
Frequency
Consequence
NM_033305.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS13A | NM_033305.3 | c.5625A>G | p.Leu1875= | synonymous_variant | 44/72 | ENST00000360280.8 | |
VPS13A | NM_001018037.2 | c.5508A>G | p.Leu1836= | synonymous_variant | 43/71 | ||
VPS13A | NM_015186.4 | c.5625A>G | p.Leu1875= | synonymous_variant | 44/69 | ||
VPS13A | NM_001018038.3 | c.5625A>G | p.Leu1875= | synonymous_variant | 44/69 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS13A | ENST00000360280.8 | c.5625A>G | p.Leu1875= | synonymous_variant | 44/72 | 1 | NM_033305.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00575 AC: 875AN: 152110Hom.: 12 Cov.: 32
GnomAD3 exomes AF: 0.00158 AC: 395AN: 250772Hom.: 6 AF XY: 0.00111 AC XY: 150AN XY: 135530
GnomAD4 exome AF: 0.000631 AC: 922AN: 1461316Hom.: 14 Cov.: 32 AF XY: 0.000579 AC XY: 421AN XY: 726934
GnomAD4 genome AF: 0.00577 AC: 878AN: 152228Hom.: 12 Cov.: 32 AF XY: 0.00550 AC XY: 409AN XY: 74426
ClinVar
Submissions by phenotype
Chorea-acanthocytosis Benign:2
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Oct 18, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at