chr2-115753250-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020868.6(DPP10):āc.1027A>Gā(p.Ile343Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000769 in 1,612,002 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_020868.6 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPP10 | NM_020868.6 | c.1027A>G | p.Ile343Val | missense_variant | 11/26 | ENST00000410059.6 | |
LOC105373572 | XR_923234.3 | n.67+1485T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPP10 | ENST00000410059.6 | c.1027A>G | p.Ile343Val | missense_variant | 11/26 | 1 | NM_020868.6 | A1 | |
DPP10 | ENST00000393147.6 | c.1039A>G | p.Ile347Val | missense_variant | 11/26 | 1 | P3 | ||
DPP10 | ENST00000310323.12 | c.1006A>G | p.Ile336Val | missense_variant | 11/26 | 1 | |||
DPP10 | ENST00000409163.5 | c.877A>G | p.Ile293Val | missense_variant | 12/27 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152128Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000152 AC: 38AN: 250440Hom.: 0 AF XY: 0.000236 AC XY: 32AN XY: 135350
GnomAD4 exome AF: 0.0000767 AC: 112AN: 1459756Hom.: 1 Cov.: 32 AF XY: 0.000107 AC XY: 78AN XY: 726194
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152246Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74448
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2022 | The c.1039A>G (p.I347V) alteration is located in exon 11 (coding exon 11) of the DPP10 gene. This alteration results from a A to G substitution at nucleotide position 1039, causing the isoleucine (I) at amino acid position 347 to be replaced by a valine (V). 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