4-121669609-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The ENST00000296511.10(ANXA5):āc.896T>Cā(p.Met299Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000205 in 1,613,474 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000079 ( 0 hom., cov: 31)
Exomes š: 0.00022 ( 0 hom. )
Consequence
ANXA5
ENST00000296511.10 missense
ENST00000296511.10 missense
Scores
4
15
Clinical Significance
Conservation
PhyloP100: 4.13
Genes affected
ANXA5 (HGNC:543): (annexin A5) The Annexin 5 gene spans 29 kb containing 13 exons, and encodes a single transcript of approximately 1.6 kb and a protein product with a molecular weight of about 35 kDa.The protein encoded by this gene belongs to the annexin family of calcium-dependent phospholipid binding proteins some of which have been implicated in membrane-related events along exocytotic and endocytotic pathways. Annexin 5 is a phospholipase A2 and protein kinase C inhibitory protein with calcium channel activity and a potential role in cellular signal transduction, inflammation, growth and differentiation. Annexin 5 has also been described as placental anticoagulant protein I, vascular anticoagulant-alpha, endonexin II, lipocortin V, placental protein 4 and anchorin CII. Polymorphisms in this gene have been implicated in various obstetric complications. [provided by RefSeq, Dec 2019]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.370552).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANXA5 | NM_001154.4 | c.896T>C | p.Met299Thr | missense_variant | 12/13 | ENST00000296511.10 | NP_001145.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANXA5 | ENST00000296511.10 | c.896T>C | p.Met299Thr | missense_variant | 12/13 | 1 | NM_001154.4 | ENSP00000296511 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152120Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000956 AC: 24AN: 251036Hom.: 0 AF XY: 0.0000884 AC XY: 12AN XY: 135680
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GnomAD4 exome AF: 0.000218 AC: 319AN: 1461354Hom.: 0 Cov.: 30 AF XY: 0.000198 AC XY: 144AN XY: 726968
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GnomAD4 genome AF: 0.0000789 AC: 12AN: 152120Hom.: 0 Cov.: 31 AF XY: 0.0000807 AC XY: 6AN XY: 74312
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2022 | The c.896T>C (p.M299T) alteration is located in exon 12 (coding exon 11) of the ANXA5 gene. This alteration results from a T to C substitution at nucleotide position 896, causing the methionine (M) at amino acid position 299 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T;T
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
B;B;B
Vest4
MVP
MPC
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