5-96952434-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005575.3(LNPEP):c.19+16260A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,034 control chromosomes in the GnomAD database, including 18,720 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 0.49 ( 18720 hom., cov: 32)
Consequence
LNPEP
NM_005575.3 intron
NM_005575.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0280
Publications
13 publications found
Genes affected
LNPEP (HGNC:6656): (leucyl and cystinyl aminopeptidase) This gene encodes a zinc-dependent aminopeptidase that cleaves vasopressin, oxytocin, lys-bradykinin, met-enkephalin, dynorphin A and other peptide hormones. The protein can be secreted in maternal serum, reside in intracellular vesicles with the insulin-responsive glucose transporter GLUT4, or form a type II integral membrane glycoprotein. The protein catalyzes the final step in the conversion of angiotensinogen to angiotensin IV (AT4) and is also a receptor for AT4. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
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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=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.494 AC: 75007AN: 151916Hom.: 18677 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
75007
AN:
151916
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.494 AC: 75114AN: 152034Hom.: 18720 Cov.: 32 AF XY: 0.491 AC XY: 36494AN XY: 74288 show subpopulations
GnomAD4 genome
AF:
AC:
75114
AN:
152034
Hom.:
Cov.:
32
AF XY:
AC XY:
36494
AN XY:
74288
show subpopulations
African (AFR)
AF:
AC:
23131
AN:
41462
American (AMR)
AF:
AC:
6527
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
AC:
1282
AN:
3470
East Asian (EAS)
AF:
AC:
2296
AN:
5174
South Asian (SAS)
AF:
AC:
2105
AN:
4818
European-Finnish (FIN)
AF:
AC:
4947
AN:
10560
Middle Eastern (MID)
AF:
AC:
124
AN:
294
European-Non Finnish (NFE)
AF:
AC:
33220
AN:
67960
Other (OTH)
AF:
AC:
1015
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1939
3877
5816
7754
9693
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
670
1340
2010
2680
3350
<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:
1839
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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