rs17087239
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005575.3(LNPEP):c.*61C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000147 in 1,579,214 control chromosomes in the GnomAD database, including 1 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 0.00068 ( 1 hom., cov: 33)
Exomes 𝑓: 0.000090 ( 0 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: 1.92
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 Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LNPEP | NM_005575.3 | c.*61C>T | 3_prime_UTR_variant | 18/18 | ENST00000231368.10 | ||
LNPEP | NM_175920.4 | c.*61C>T | 3_prime_UTR_variant | 18/18 | |||
LNPEP | XM_047417177.1 | c.*61C>T | 3_prime_UTR_variant | 16/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LNPEP | ENST00000231368.10 | c.*61C>T | 3_prime_UTR_variant | 18/18 | 1 | NM_005575.3 | P1 | ||
LNPEP | ENST00000395770.3 | c.*61C>T | 3_prime_UTR_variant | 18/18 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000677 AC: 103AN: 152146Hom.: 1 Cov.: 33
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GnomAD4 exome AF: 0.0000897 AC: 128AN: 1426950Hom.: 0 Cov.: 25 AF XY: 0.0000986 AC XY: 70AN XY: 710266
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GnomAD4 genome ? AF: 0.000683 AC: 104AN: 152264Hom.: 1 Cov.: 33 AF XY: 0.000685 AC XY: 51AN XY: 74442
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ClinVar
Not reported inComputational scores
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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