rs17239917
Variant names:
Variant summary
Our verdict is Benign. The variant received -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
Publications
12 publications found
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]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANPEP | NM_001150.3 | c.2670-79C>T | intron_variant | Intron 19 of 20 | ENST00000300060.7 | NP_001141.2 | ||
ANPEP | NM_001381923.1 | c.2670-79C>T | intron_variant | Intron 19 of 20 | NP_001368852.1 | |||
ANPEP | NM_001381924.1 | c.2670-79C>T | intron_variant | Intron 18 of 19 | NP_001368853.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANPEP | ENST00000300060.7 | c.2670-79C>T | intron_variant | Intron 19 of 20 | 1 | NM_001150.3 | ENSP00000300060.6 | |||
ANPEP | ENST00000559874.2 | c.2670-79C>T | intron_variant | Intron 19 of 20 | 3 | ENSP00000452934.2 | ||||
ANPEP | ENST00000560137.2 | c.2670-79C>T | intron_variant | Intron 19 of 20 | 3 | ENSP00000453413.2 | ||||
ANPEP | ENST00000679248.1 | c.2670-79C>T | intron_variant | Intron 20 of 21 | ENSP00000502886.1 |
Frequencies
GnomAD3 genomes AF: 0.140 AC: 21356AN: 152074Hom.: 1670 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
21356
AN:
152074
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.168 AC: 190943AN: 1138038Hom.: 17495 AF XY: 0.169 AC XY: 97896AN XY: 577844 show subpopulations
GnomAD4 exome
AF:
AC:
190943
AN:
1138038
Hom.:
AF XY:
AC XY:
97896
AN XY:
577844
show subpopulations
African (AFR)
AF:
AC:
2670
AN:
26926
American (AMR)
AF:
AC:
3292
AN:
39870
Ashkenazi Jewish (ASJ)
AF:
AC:
4627
AN:
23676
East Asian (EAS)
AF:
AC:
27
AN:
37560
South Asian (SAS)
AF:
AC:
13675
AN:
77100
European-Finnish (FIN)
AF:
AC:
7072
AN:
51024
Middle Eastern (MID)
AF:
AC:
1179
AN:
5110
European-Non Finnish (NFE)
AF:
AC:
150221
AN:
827056
Other (OTH)
AF:
AC:
8180
AN:
49716
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
7752
15503
23255
31006
38758
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
4628
9256
13884
18512
23140
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.140 AC: 21354AN: 152192Hom.: 1669 Cov.: 32 AF XY: 0.138 AC XY: 10271AN XY: 74402 show subpopulations
GnomAD4 genome
AF:
AC:
21354
AN:
152192
Hom.:
Cov.:
32
AF XY:
AC XY:
10271
AN XY:
74402
show subpopulations
African (AFR)
AF:
AC:
3993
AN:
41514
American (AMR)
AF:
AC:
1679
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
AC:
671
AN:
3466
East Asian (EAS)
AF:
AC:
8
AN:
5178
South Asian (SAS)
AF:
AC:
774
AN:
4818
European-Finnish (FIN)
AF:
AC:
1467
AN:
10612
Middle Eastern (MID)
AF:
AC:
51
AN:
294
European-Non Finnish (NFE)
AF:
AC:
12350
AN:
67992
Other (OTH)
AF:
AC:
341
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
917
1834
2751
3668
4585
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
248
496
744
992
1240
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
254
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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