chr12-121004396-T-A
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_022895.3(C12orf43):c.546A>T(p.Thr182Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 1,613,802 control chromosomes in the GnomAD database, including 77,533 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.30 ( 7005 hom., cov: 32)
Exomes 𝑓: 0.30 ( 70528 hom. )
Consequence
C12orf43
NM_022895.3 synonymous
NM_022895.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.929
Genes affected
C12orf43 (HGNC:25719): (chromosome 12 open reading frame 43) Predicted to be involved in Spemann organizer formation and negative regulation of Wnt signaling pathway. Predicted to be located in nuclear envelope. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP7
Synonymous conserved (PhyloP=-0.929 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
C12orf43 | NM_022895.3 | c.546A>T | p.Thr182Thr | synonymous_variant | 6/6 | ENST00000288757.7 | NP_075046.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
C12orf43 | ENST00000288757.7 | c.546A>T | p.Thr182Thr | synonymous_variant | 6/6 | 1 | NM_022895.3 | ENSP00000288757.5 |
Frequencies
GnomAD3 genomes AF: 0.300 AC: 45603AN: 151982Hom.: 6996 Cov.: 32
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GnomAD3 exomes AF: 0.270 AC: 67908AN: 251312Hom.: 10054 AF XY: 0.268 AC XY: 36451AN XY: 135844
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GnomAD4 exome AF: 0.305 AC: 445806AN: 1461700Hom.: 70528 Cov.: 43 AF XY: 0.300 AC XY: 218362AN XY: 727164
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GnomAD4 genome AF: 0.300 AC: 45642AN: 152102Hom.: 7005 Cov.: 32 AF XY: 0.296 AC XY: 21999AN XY: 74330
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Not reported inComputational scores
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CADD
Benign
DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at