chr16-67975917-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001370198.1(DPEP3):c.1315G>A(p.Val439Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000119 in 1,613,912 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001370198.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DPEP3 | NM_001370198.1 | c.1315G>A | p.Val439Met | missense_variant | Exon 10 of 10 | ENST00000268793.6 | NP_001357127.1 | |
DPEP3 | NM_001129758.2 | c.1312G>A | p.Val438Met | missense_variant | Exon 10 of 10 | NP_001123230.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DPEP3 | ENST00000268793.6 | c.1315G>A | p.Val439Met | missense_variant | Exon 10 of 10 | 1 | NM_001370198.1 | ENSP00000268793.5 | ||
DPEP3 | ENST00000672962.1 | c.1390G>A | p.Val464Met | missense_variant | Exon 10 of 10 | ENSP00000500237.1 |
Frequencies
GnomAD3 genomes AF: 0.000309 AC: 47AN: 152156Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000104 AC: 26AN: 250650Hom.: 0 AF XY: 0.0000811 AC XY: 11AN XY: 135568
GnomAD4 exome AF: 0.0000985 AC: 144AN: 1461638Hom.: 0 Cov.: 31 AF XY: 0.0000963 AC XY: 70AN XY: 727086
GnomAD4 genome AF: 0.000315 AC: 48AN: 152274Hom.: 0 Cov.: 33 AF XY: 0.000255 AC XY: 19AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1390G>A (p.V464M) alteration is located in exon 10 (coding exon 10) of the DPEP3 gene. This alteration results from a G to A substitution at nucleotide position 1390, causing the valine (V) at amino acid position 464 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