chr4-78592061-A-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005139.3(ANXA3):c.483+438A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 151,982 control chromosomes in the GnomAD database, including 26,869 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 0.59 ( 26869 hom., cov: 32)
Consequence
ANXA3
NM_005139.3 intron
NM_005139.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0820
Genes affected
ANXA3 (HGNC:541): (annexin A3) This gene encodes a member of the annexin family. Members of this calcium-dependent phospholipid-binding protein family play a role in the regulation of cellular growth and in signal transduction pathways. This protein functions in the inhibition of phopholipase A2 and cleavage of inositol 1,2-cyclic phosphate to form inositol 1-phosphate. This protein may also play a role in anti-coagulation. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANXA3 | NM_005139.3 | c.483+438A>G | intron_variant | ENST00000264908.11 | NP_005130.1 | |||
ANXA3 | XM_047450154.1 | c.483+438A>G | intron_variant | XP_047306110.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANXA3 | ENST00000264908.11 | c.483+438A>G | intron_variant | 1 | NM_005139.3 | ENSP00000264908 | P1 | |||
ANXA3 | ENST00000503570.6 | c.366+438A>G | intron_variant | 5 | ENSP00000421015 | |||||
ANXA3 | ENST00000512542.5 | c.16-3320A>G | intron_variant | 3 | ENSP00000426591 | |||||
ANXA3 | ENST00000512884.5 | c.366+438A>G | intron_variant | 5 | ENSP00000423068 |
Frequencies
GnomAD3 genomes AF: 0.591 AC: 89730AN: 151866Hom.: 26864 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.591 AC: 89787AN: 151982Hom.: 26869 Cov.: 32 AF XY: 0.587 AC XY: 43621AN XY: 74268
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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