rs17239917
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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.2670-79C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 1,290,230 control chromosomes in the GnomAD database, including 19,164 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 0.14 ( 1669 hom., cov: 32)
Exomes 𝑓: 0.17 ( 17495 hom. )
Consequence
ANPEP
NM_001150.3 intron
NM_001150.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.351
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=-0.81).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANPEP | NM_001150.3 | c.2670-79C>T | intron_variant | ENST00000300060.7 | |||
ANPEP | NM_001381923.1 | c.2670-79C>T | intron_variant | ||||
ANPEP | NM_001381924.1 | c.2670-79C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANPEP | ENST00000300060.7 | c.2670-79C>T | intron_variant | 1 | NM_001150.3 | P1 | |||
ANPEP | ENST00000559874.2 | c.2670-79C>T | intron_variant | 3 | P1 | ||||
ANPEP | ENST00000560137.2 | c.2670-79C>T | intron_variant | 3 | P1 | ||||
ANPEP | ENST00000679248.1 | c.2670-79C>T | intron_variant | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.140 AC: 21356AN: 152074Hom.: 1670 Cov.: 32
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GnomAD4 exome AF: 0.168 AC: 190943AN: 1138038Hom.: 17495 AF XY: 0.169 AC XY: 97896AN XY: 577844
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GnomAD4 genome ? AF: 0.140 AC: 21354AN: 152192Hom.: 1669 Cov.: 32 AF XY: 0.138 AC XY: 10271AN XY: 74402
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3478
ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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