chr16-30066927-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001243177.4(ALDOA):c.30C>T(p.Ser10=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000503 in 1,550,860 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000079 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000047 ( 0 hom. )
Consequence
ALDOA
NM_001243177.4 synonymous
NM_001243177.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.27
Genes affected
ALDOA (HGNC:414): (aldolase, fructose-bisphosphate A) This gene encodes a member of the class I fructose-bisphosphate aldolase protein family. The encoded protein is a glycolytic enzyme that catalyzes the reversible conversion of fructose-1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. Three aldolase isozymes (A, B, and C), encoded by three different genes, are differentially expressed during development. Mutations in this gene have been associated with Glycogen Storage Disease XII, an autosomal recessive disorder associated with hemolytic anemia. Disruption of this gene also plays a role in the progression of multiple types of cancers. Related pseudogenes have been identified on chromosomes 3 and 10. [provided by RefSeq, Sep 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
?
Variant 16-30066927-C-T is Benign according to our data. Variant chr16-30066927-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3040743.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=3.27 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALDOA | NM_001243177.4 | c.30C>T | p.Ser10= | synonymous_variant | 2/10 | ENST00000642816.3 | |
LOC112694756 | NM_001365304.2 | c.*489-307C>T | intron_variant | ENST00000338110.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALDOA | ENST00000642816.3 | c.30C>T | p.Ser10= | synonymous_variant | 2/10 | NM_001243177.4 | |||
ENST00000338110.11 | c.*489-307C>T | intron_variant | 1 | NM_001365304.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152236Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000536 AC: 8AN: 149320Hom.: 0 AF XY: 0.0000373 AC XY: 3AN XY: 80404
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GnomAD4 exome AF: 0.0000472 AC: 66AN: 1398506Hom.: 0 Cov.: 31 AF XY: 0.0000435 AC XY: 30AN XY: 689778
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GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152354Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74508
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
ALDOA-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 17, 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
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Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at