rs623980
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020383.4(XPNPEP1):c.653-48T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 1,574,810 control chromosomes in the GnomAD database, including 251,906 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 0.50 ( 19736 hom., cov: 33)
Exomes 𝑓: 0.56 ( 232170 hom. )
Consequence
XPNPEP1
NM_020383.4 intron
NM_020383.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.09
Genes affected
XPNPEP1 (HGNC:12822): (X-prolyl aminopeptidase 1) This gene encodes the cytosolic form of a metalloaminopeptidase that catalyzes the cleavage of the N-terminal amino acid adjacent to a proline residue. The gene product may play a role in degradation and maturation of tachykinins, neuropeptides, and peptide hormones. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Nov 2009]
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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=-0.83).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XPNPEP1 | NM_020383.4 | c.653-48T>C | intron_variant | ENST00000502935.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XPNPEP1 | ENST00000502935.6 | c.653-48T>C | intron_variant | 1 | NM_020383.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.496 AC: 75382AN: 151986Hom.: 19734 Cov.: 33
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GnomAD3 exomes AF: 0.478 AC: 108144AN: 226460Hom.: 27986 AF XY: 0.478 AC XY: 58327AN XY: 121928
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GnomAD4 exome AF: 0.561 AC: 798578AN: 1422706Hom.: 232170 Cov.: 23 AF XY: 0.555 AC XY: 392798AN XY: 708196
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GnomAD4 genome ? AF: 0.496 AC: 75398AN: 152104Hom.: 19736 Cov.: 33 AF XY: 0.487 AC XY: 36203AN XY: 74378
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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
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