rs147023941
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_016222.4(DDX41):c.1233G>A(p.Glu411=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00115 in 1,613,452 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_016222.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDX41 | NM_016222.4 | c.1233G>A | p.Glu411= | splice_region_variant, synonymous_variant | 12/17 | ENST00000330503.12 | |
DDX41 | NM_001321732.2 | c.855G>A | p.Glu285= | splice_region_variant, synonymous_variant | 11/16 | ||
DDX41 | NM_001321830.2 | c.855G>A | p.Glu285= | splice_region_variant, synonymous_variant | 12/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDX41 | ENST00000330503.12 | c.1233G>A | p.Glu411= | splice_region_variant, synonymous_variant | 12/17 | 1 | NM_016222.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00141 AC: 214AN: 152198Hom.: 6 Cov.: 33
GnomAD3 exomes AF: 0.00218 AC: 546AN: 250622Hom.: 12 AF XY: 0.00209 AC XY: 283AN XY: 135446
GnomAD4 exome AF: 0.00112 AC: 1636AN: 1461254Hom.: 26 Cov.: 34 AF XY: 0.00114 AC XY: 830AN XY: 726944
GnomAD4 genome ? AF: 0.00141 AC: 214AN: 152198Hom.: 6 Cov.: 33 AF XY: 0.00128 AC XY: 95AN XY: 74342
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 04, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 09, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at