chr15-89785320-G-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001150.3(ANPEP):c.*29C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 1,612,628 control chromosomes in the GnomAD database, including 263,185 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 0.60 ( 29698 hom., cov: 32)
Exomes 𝑓: 0.56 ( 233487 hom. )
Consequence
ANPEP
NM_001150.3 3_prime_UTR
NM_001150.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.155
Genes affected
ANPEP (HGNC:500): (alanyl aminopeptidase, membrane) Aminopeptidase N is located in the small-intestinal and renal microvillar membrane, and also in other plasma membranes. In the small intestine aminopeptidase N plays a role in the final digestion of peptides generated from hydrolysis of proteins by gastric and pancreatic proteases. Its function in proximal tubular epithelial cells and other cell types is less clear. The large extracellular carboxyterminal domain contains a pentapeptide consensus sequence characteristic of members of the zinc-binding metalloproteinase superfamily. Sequence comparisons with known enzymes of this class showed that CD13 and aminopeptidase N are identical. The latter enzyme was thought to be involved in the metabolism of regulatory peptides by diverse cell types, including small intestinal and renal tubular epithelial cells, macrophages, granulocytes, and synaptic membranes from the CNS. This membrane-bound zinc metalloprotease is known to serve as a receptor for the HCoV-229E alphacoronavirus as well as other non-human coronaviruses. This gene has also been shown to promote angiogenesis, tumor growth, and metastasis and defects in this gene are associated with various types of leukemia and lymphoma. [provided by RefSeq, Apr 2020]
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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=-0.82).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANPEP | NM_001150.3 | c.*29C>G | 3_prime_UTR_variant | 21/21 | ENST00000300060.7 | ||
ANPEP | NM_001381923.1 | c.*29C>G | 3_prime_UTR_variant | 21/21 | |||
ANPEP | NM_001381924.1 | c.*29C>G | 3_prime_UTR_variant | 20/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANPEP | ENST00000300060.7 | c.*29C>G | 3_prime_UTR_variant | 21/21 | 1 | NM_001150.3 | P1 | ||
ANPEP | ENST00000559874.2 | c.*29C>G | 3_prime_UTR_variant | 21/21 | 3 | P1 | |||
ANPEP | ENST00000560137.2 | c.*29C>G | 3_prime_UTR_variant | 21/21 | 3 | P1 | |||
ANPEP | ENST00000679248.1 | c.*29C>G | 3_prime_UTR_variant | 22/22 | P1 |
Frequencies
GnomAD3 genomes AF: 0.604 AC: 91696AN: 151898Hom.: 29661 Cov.: 32
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GnomAD3 exomes AF: 0.521 AC: 130804AN: 250912Hom.: 36737 AF XY: 0.531 AC XY: 71997AN XY: 135634
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GnomAD4 exome AF: 0.558 AC: 815078AN: 1460612Hom.: 233487 Cov.: 42 AF XY: 0.561 AC XY: 407629AN XY: 726516
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GnomAD4 genome AF: 0.604 AC: 91784AN: 152016Hom.: 29698 Cov.: 32 AF XY: 0.589 AC XY: 43779AN XY: 74314
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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