chr2-219423818-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM2PP3
The NM_001927.4(DES):c.1286G>T(p.Arg429Leu) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,106 control chromosomes in the GnomAD database, with no homozygous occurrence. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R429Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001927.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DES | NM_001927.4 | c.1286G>T | p.Arg429Leu | missense_variant, splice_region_variant | 7/9 | ENST00000373960.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DES | ENST00000373960.4 | c.1286G>T | p.Arg429Leu | missense_variant, splice_region_variant | 7/9 | 1 | NM_001927.4 | P1 | |
DES | ENST00000477226.6 | n.760G>T | splice_region_variant, non_coding_transcript_exon_variant | 6/8 | 4 | ||||
DES | ENST00000492726.1 | n.681G>T | non_coding_transcript_exon_variant | 6/6 | 4 | ||||
DES | ENST00000683013.1 | n.674G>T | splice_region_variant, non_coding_transcript_exon_variant | 5/7 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152106Hom.: 0 Cov.: 31
GnomAD4 exome Cov.: 31
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152106Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74300
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at