rs9127
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.*7928G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 151,918 control chromosomes in the GnomAD database, including 22,394 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 0.54 ( 22391 hom., cov: 32)
Exomes 𝑓: 0.36 ( 3 hom. )
Consequence
LNPEP
NM_005575.3 3_prime_UTR
NM_005575.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.754
Publications
33 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=-0.82).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LNPEP | NM_005575.3 | c.*7928G>A | 3_prime_UTR_variant | Exon 18 of 18 | ENST00000231368.10 | NP_005566.2 | ||
LNPEP | NM_175920.4 | c.*7928G>A | 3_prime_UTR_variant | Exon 18 of 18 | NP_787116.2 | |||
LNPEP | XM_047417177.1 | c.*7928G>A | 3_prime_UTR_variant | Exon 16 of 16 | XP_047273133.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.541 AC: 82083AN: 151772Hom.: 22389 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
82083
AN:
151772
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: 0.357 AC: 10AN: 28Hom.: 3 Cov.: 0 AF XY: 0.389 AC XY: 7AN XY: 18 show subpopulations
GnomAD4 exome
AF:
AC:
10
AN:
28
Hom.:
Cov.:
0
AF XY:
AC XY:
7
AN XY:
18
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
AC:
3
AN:
6
Middle Eastern (MID)
AF:
AC:
2
AN:
2
European-Non Finnish (NFE)
AF:
AC:
4
AN:
16
Other (OTH)
AF:
AC:
1
AN:
4
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.438
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.541 AC: 82109AN: 151890Hom.: 22391 Cov.: 32 AF XY: 0.546 AC XY: 40552AN XY: 74224 show subpopulations
GnomAD4 genome
AF:
AC:
82109
AN:
151890
Hom.:
Cov.:
32
AF XY:
AC XY:
40552
AN XY:
74224
show subpopulations
African (AFR)
AF:
AC:
20556
AN:
41398
American (AMR)
AF:
AC:
9287
AN:
15242
Ashkenazi Jewish (ASJ)
AF:
AC:
2331
AN:
3466
East Asian (EAS)
AF:
AC:
3214
AN:
5176
South Asian (SAS)
AF:
AC:
3306
AN:
4820
European-Finnish (FIN)
AF:
AC:
5943
AN:
10560
Middle Eastern (MID)
AF:
AC:
184
AN:
294
European-Non Finnish (NFE)
AF:
AC:
35704
AN:
67918
Other (OTH)
AF:
AC:
1147
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1967
3933
5900
7866
9833
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1968
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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