rs3756618
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005575.3(LNPEP):c.*501T>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 0.0143 in 152,916 control chromosomes in the GnomAD database, including 52 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 0.014 ( 52 hom., cov: 32)
Exomes 𝑓: 0.0085 ( 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: 0.261
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=-0.84).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0809 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LNPEP | NM_005575.3 | c.*501T>A | 3_prime_UTR_variant | 18/18 | ENST00000231368.10 | ||
LNPEP | NM_175920.4 | c.*501T>A | 3_prime_UTR_variant | 18/18 | |||
LNPEP | XM_047417177.1 | c.*501T>A | 3_prime_UTR_variant | 16/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LNPEP | ENST00000231368.10 | c.*501T>A | 3_prime_UTR_variant | 18/18 | 1 | NM_005575.3 | P1 | ||
LNPEP | ENST00000395770.3 | c.*501T>A | 3_prime_UTR_variant | 18/18 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0143 AC: 2180AN: 152208Hom.: 52 Cov.: 32
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GnomAD4 exome AF: 0.00847 AC: 5AN: 590Hom.: 0 Cov.: 0 AF XY: 0.00617 AC XY: 2AN XY: 324
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GnomAD4 genome ? AF: 0.0143 AC: 2182AN: 152326Hom.: 52 Cov.: 32 AF XY: 0.0168 AC XY: 1250AN XY: 74484
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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