1-111765791-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007204.5(DDX20):c.1367A>G(p.Lys456Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000534 in 1,611,210 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★).
Frequency
Consequence
NM_007204.5 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 |
---|---|---|---|---|---|---|---|
DDX20 | NM_007204.5 | c.1367A>G | p.Lys456Arg | missense_variant | 11/11 | ENST00000369702.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDX20 | ENST00000369702.5 | c.1367A>G | p.Lys456Arg | missense_variant | 11/11 | 1 | NM_007204.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000169 AC: 42AN: 248296Hom.: 0 AF XY: 0.000164 AC XY: 22AN XY: 134078
GnomAD4 exome AF: 0.0000541 AC: 79AN: 1458930Hom.: 0 Cov.: 30 AF XY: 0.0000524 AC XY: 38AN XY: 725526
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2023 | The c.1367A>G (p.K456R) alteration is located in exon 11 (coding exon 11) of the DDX20 gene. This alteration results from a A to G substitution at nucleotide position 1367, causing the lysine (K) at amino acid position 456 to be replaced by an arginine (R). 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