1-150983422-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003568.3(ANXA9):āc.160A>Gā(p.Ile54Val) variant causes a missense change. The variant allele was found at a frequency of 0.000259 in 1,611,474 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00036 ( 0 hom., cov: 32)
Exomes š: 0.00025 ( 1 hom. )
Consequence
ANXA9
NM_003568.3 missense
NM_003568.3 missense
Scores
6
13
Clinical Significance
Conservation
PhyloP100: 4.25
Genes affected
ANXA9 (HGNC:547): (annexin A9) The annexins are a family of calcium-dependent phospholipid-binding proteins. Members of the annexin family contain 4 internal repeat domains, each of which includes a type II calcium-binding site. The calcium-binding sites are required for annexins to aggregate and cooperatively bind anionic phospholipids and extracellular matrix proteins. This gene encodes a divergent member of the annexin protein family in which all four homologous type II calcium-binding sites in the conserved tetrad core contain amino acid substitutions that ablate their function. However, structural analysis suggests that the conserved putative ion channel formed by the tetrad core is intact. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.21541587).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANXA9 | NM_003568.3 | c.160A>G | p.Ile54Val | missense_variant | 4/14 | ENST00000368947.9 | NP_003559.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANXA9 | ENST00000368947.9 | c.160A>G | p.Ile54Val | missense_variant | 4/14 | 1 | NM_003568.3 | ENSP00000357943 | P1 | |
ANXA9 | ENST00000474997.1 | n.313A>G | non_coding_transcript_exon_variant | 3/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000361 AC: 55AN: 152250Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000263 AC: 64AN: 243428Hom.: 0 AF XY: 0.000281 AC XY: 37AN XY: 131590
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GnomAD4 exome AF: 0.000249 AC: 363AN: 1459106Hom.: 1 Cov.: 31 AF XY: 0.000269 AC XY: 195AN XY: 725554
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GnomAD4 genome AF: 0.000361 AC: 55AN: 152368Hom.: 0 Cov.: 32 AF XY: 0.000349 AC XY: 26AN XY: 74514
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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 | Sep 01, 2021 | The c.160A>G (p.I54V) alteration is located in exon 4 (coding exon 2) of the ANXA9 gene. This alteration results from a A to G substitution at nucleotide position 160, causing the isoleucine (I) at amino acid position 54 to be replaced by a valine (V). 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
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Uncertain
T
Polyphen
P
Vest4
MVP
MPC
ClinPred
T
GERP RS
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