rs1057808
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005575.3(LNPEP):c.*408T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.038 in 174,162 control chromosomes in the GnomAD database, including 204 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 0.037 ( 184 hom., cov: 32)
Exomes 𝑓: 0.043 ( 20 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: 0.193
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 made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0537 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LNPEP | NM_005575.3 | c.*408T>C | 3_prime_UTR_variant | 18/18 | ENST00000231368.10 | ||
LNPEP | NM_175920.4 | c.*408T>C | 3_prime_UTR_variant | 18/18 | |||
LNPEP | XM_047417177.1 | c.*408T>C | 3_prime_UTR_variant | 16/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LNPEP | ENST00000231368.10 | c.*408T>C | 3_prime_UTR_variant | 18/18 | 1 | NM_005575.3 | P1 | ||
LNPEP | ENST00000395770.3 | c.*408T>C | 3_prime_UTR_variant | 18/18 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0374 AC: 5694AN: 152158Hom.: 185 Cov.: 32
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GnomAD4 exome AF: 0.0427 AC: 935AN: 21886Hom.: 20 Cov.: 0 AF XY: 0.0411 AC XY: 453AN XY: 11034
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GnomAD4 genome ? AF: 0.0374 AC: 5690AN: 152276Hom.: 184 Cov.: 32 AF XY: 0.0356 AC XY: 2648AN XY: 74448
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at