2-115343900-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020868.6(DPP10):c.259C>T(p.Arg87Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000441 in 1,610,268 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. 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. R87Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_020868.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPP10 | NM_020868.6 | c.259C>T | p.Arg87Trp | missense_variant | 3/26 | ENST00000410059.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPP10 | ENST00000410059.6 | c.259C>T | p.Arg87Trp | missense_variant | 3/26 | 1 | NM_020868.6 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000119 AC: 18AN: 151786Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000100 AC: 25AN: 248822Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 134566
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1458364Hom.: 0 Cov.: 29 AF XY: 0.0000345 AC XY: 25AN XY: 725482
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 151904Hom.: 0 Cov.: 31 AF XY: 0.0000943 AC XY: 7AN XY: 74222
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2023 | The c.271C>T (p.R91W) alteration is located in exon 3 (coding exon 3) of the DPP10 gene. This alteration results from a C to T substitution at nucleotide position 271, causing the arginine (R) at amino acid position 91 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