chr11-43326580-C-T
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001142930.2(API5):c.824C>T(p.Thr275Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000746 in 1,608,664 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 Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
API5
NM_001142930.2 missense
NM_001142930.2 missense
Scores
7
10
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.37
Genes affected
API5 (HGNC:594): (apoptosis inhibitor 5) This gene encodes an apoptosis inhibitory protein whose expression prevents apoptosis after growth factor deprivation. This protein suppresses the transcription factor E2F1-induced apoptosis and also interacts with, and negatively regulates Acinus, a nuclear factor involved in apoptotic DNA fragmentation. Its depletion enhances the cytotoxic action of the chemotherapeutic drugs. Multiple alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.21179417).
BS2
High AC in GnomAd4 at 8 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
API5 | NM_001142930.2 | c.824C>T | p.Thr275Ile | missense_variant | 7/14 | ENST00000531273.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
API5 | ENST00000531273.6 | c.824C>T | p.Thr275Ile | missense_variant | 7/14 | 2 | NM_001142930.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152150Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248066Hom.: 0 AF XY: 0.00000746 AC XY: 1AN XY: 134050
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GnomAD4 exome AF: 0.00000275 AC: 4AN: 1456514Hom.: 0 Cov.: 28 AF XY: 0.00000276 AC XY: 2AN XY: 724454
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GnomAD4 genome AF: 0.0000526 AC: 8AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74328
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
N;N;N;N;N
REVEL
Benign
Sift
Uncertain
D;D;D;D;D
Sift4G
Benign
T;D;D;D;D
Polyphen
0.53, 0.34
.;P;.;B;B
Vest4
MutPred
0.61
.;Gain of sheet (P = 0.0101);.;Gain of sheet (P = 0.0101);Gain of sheet (P = 0.0101);
MVP
MPC
0.88
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at