chr12-56282971-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_004077.3(CS):c.288T>C(p.Phe96=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000225 in 1,614,200 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 Benign (★).
Frequency
Genomes: 𝑓 0.0012 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00013 ( 0 hom. )
Consequence
CS
NM_004077.3 synonymous
NM_004077.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.03
Genes affected
CS (HGNC:2422): (citrate synthase) The protein encoded by this gene is a Krebs tricarboxylic acid cycle enzyme that catalyzes the synthesis of citrate from oxaloacetate and acetyl coenzyme A. The enzyme is found in nearly all cells capable of oxidative metablism. This protein is nuclear encoded and transported into the mitochondrial matrix, where the mature form is found. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
?
Variant 12-56282971-A-G is Benign according to our data. Variant chr12-56282971-A-G is described in ClinVar as [Benign]. Clinvar id is 728964.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=2.03 with no splicing effect.
BS2
?
High AC in GnomAd at 177 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CS | NM_004077.3 | c.288T>C | p.Phe96= | synonymous_variant | 5/11 | ENST00000351328.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CS | ENST00000351328.8 | c.288T>C | p.Phe96= | synonymous_variant | 5/11 | 1 | NM_004077.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00116 AC: 177AN: 152208Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000286 AC: 72AN: 251466Hom.: 0 AF XY: 0.000199 AC XY: 27AN XY: 135908
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GnomAD4 exome AF: 0.000127 AC: 186AN: 1461874Hom.: 0 Cov.: 31 AF XY: 0.000113 AC XY: 82AN XY: 727238
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GnomAD4 genome ? AF: 0.00116 AC: 177AN: 152326Hom.: 0 Cov.: 32 AF XY: 0.00109 AC XY: 81AN XY: 74498
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 04, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at