chr15-89801528-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001150.3(ANPEP):c.1649C>T(p.Pro550Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000805 in 1,614,082 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001150.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANPEP | NM_001150.3 | c.1649C>T | p.Pro550Leu | missense_variant | 11/21 | ENST00000300060.7 | |
ANPEP | NM_001381923.1 | c.1649C>T | p.Pro550Leu | missense_variant | 11/21 | ||
ANPEP | NM_001381924.1 | c.1649C>T | p.Pro550Leu | missense_variant | 10/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANPEP | ENST00000300060.7 | c.1649C>T | p.Pro550Leu | missense_variant | 11/21 | 1 | NM_001150.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251438Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135898
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461866Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727234
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2023 | The c.1649C>T (p.P550L) alteration is located in exon 11 (coding exon 10) of the ANPEP gene. This alteration results from a C to T substitution at nucleotide position 1649, causing the proline (P) at amino acid position 550 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at