16-89636538-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001389466.1(DPEP1):c.376C>T(p.Arg126Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000633 in 1,612,102 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R126G) has been classified as Uncertain significance.
Frequency
Consequence
NM_001389466.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DPEP1 | NM_001389466.1 | c.376C>T | p.Arg126Trp | missense_variant | Exon 5 of 11 | ENST00000690203.1 | NP_001376395.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000523 AC: 13AN: 248378Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 134956
GnomAD4 exome AF: 0.0000644 AC: 94AN: 1459802Hom.: 0 Cov.: 34 AF XY: 0.0000592 AC XY: 43AN XY: 726166
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152300Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.376C>T (p.R126W) alteration is located in exon 5 (coding exon 4) of the DPEP1 gene. This alteration results from a C to T substitution at nucleotide position 376, causing the arginine (R) at amino acid position 126 to be replaced by a tryptophan (W). 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