1-200666422-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001031725.6(DDX59):āc.319A>Gā(p.Ile107Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0849 in 1,614,044 control chromosomes in the GnomAD database, including 10,390 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001031725.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDX59 | NM_001031725.6 | c.319A>G | p.Ile107Val | missense_variant | 2/8 | ENST00000331314.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDX59 | ENST00000331314.11 | c.319A>G | p.Ile107Val | missense_variant | 2/8 | 1 | NM_001031725.6 | P1 | |
DDX59 | ENST00000447706.6 | c.319A>G | p.Ile107Val | missense_variant | 2/8 | 2 | |||
DDX59 | ENST00000436897.1 | c.319A>G | p.Ile107Val | missense_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.118 AC: 17996AN: 152060Hom.: 1547 Cov.: 32
GnomAD3 exomes AF: 0.136 AC: 34204AN: 251350Hom.: 3723 AF XY: 0.129 AC XY: 17503AN XY: 135858
GnomAD4 exome AF: 0.0815 AC: 119085AN: 1461866Hom.: 8841 Cov.: 31 AF XY: 0.0828 AC XY: 60209AN XY: 727232
GnomAD4 genome AF: 0.118 AC: 18020AN: 152178Hom.: 1549 Cov.: 32 AF XY: 0.126 AC XY: 9386AN XY: 74384
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at