rs8037326
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004039.3(ANXA2):c.778+70G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 974,258 control chromosomes in the GnomAD database, including 283,955 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 0.79 ( 47869 hom., cov: 31)
Exomes 𝑓: 0.75 ( 236086 hom. )
Consequence
ANXA2
NM_004039.3 intron
NM_004039.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.80
Genes affected
ANXA2 (HGNC:537): (annexin A2) 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 as an autocrine factor which heightens osteoclast formation and bone resorption. This gene has three pseudogenes located on chromosomes 4, 9 and 10, respectively. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. Annexin A2 expression has been found to correlate with resistance to treatment against various cancer forms. [provided by RefSeq, Dec 2019]
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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=-0.88).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANXA2 | NM_004039.3 | c.778+70G>C | intron_variant | ENST00000451270.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANXA2 | ENST00000451270.7 | c.778+70G>C | intron_variant | 1 | NM_004039.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.790 AC: 120007AN: 151980Hom.: 47805 Cov.: 31
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GnomAD4 exome AF: 0.755 AC: 620401AN: 822160Hom.: 236086 Cov.: 11 AF XY: 0.751 AC XY: 325554AN XY: 433234
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GnomAD4 genome ? AF: 0.790 AC: 120137AN: 152098Hom.: 47869 Cov.: 31 AF XY: 0.786 AC XY: 58423AN XY: 74370
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at