chr20-58694528-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_024663.4(NPEPL1):c.443C>T(p.Thr148Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000254 in 1,613,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024663.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NPEPL1 | NM_024663.4 | c.443C>T | p.Thr148Met | missense_variant | Exon 3 of 12 | ENST00000356091.11 | NP_078939.3 | |
NPEPL1 | NM_001204872.2 | c.359C>T | p.Thr120Met | missense_variant | Exon 4 of 13 | NP_001191801.1 | ||
NPEPL1 | NM_001204873.2 | c.299C>T | p.Thr100Met | missense_variant | Exon 4 of 13 | NP_001191802.1 | ||
STX16-NPEPL1 | NR_037945.1 | n.2329C>T | non_coding_transcript_exon_variant | Exon 13 of 23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPEPL1 | ENST00000356091.11 | c.443C>T | p.Thr148Met | missense_variant | Exon 3 of 12 | 1 | NM_024663.4 | ENSP00000348395.6 | ||
STX16-NPEPL1 | ENST00000530122.1 | n.*426C>T | non_coding_transcript_exon_variant | Exon 13 of 23 | 5 | ENSP00000457522.1 | ||||
STX16-NPEPL1 | ENST00000530122.1 | n.*426C>T | 3_prime_UTR_variant | Exon 13 of 23 | 5 | ENSP00000457522.1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152240Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 249014Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135134
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461644Hom.: 0 Cov.: 31 AF XY: 0.0000261 AC XY: 19AN XY: 727110
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152240Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.443C>T (p.T148M) alteration is located in exon 3 (coding exon 3) of the NPEPL1 gene. This alteration results from a C to T substitution at nucleotide position 443, causing the threonine (T) at amino acid position 148 to be replaced by a methionine (M). 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