10-68967023-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The ENST00000354185.9(DDX21):c.910C>T(p.Arg304Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000033 in 1,605,698 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R304H) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000354185.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DDX21 | NM_004728.4 | c.910C>T | p.Arg304Cys | missense_variant | 6/15 | ENST00000354185.9 | NP_004719.2 | |
DDX21 | NM_001410932.1 | c.910C>T | p.Arg304Cys | missense_variant | 6/14 | NP_001397861.1 | ||
DDX21 | NM_001256910.2 | c.706C>T | p.Arg236Cys | missense_variant | 6/15 | NP_001243839.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DDX21 | ENST00000354185.9 | c.910C>T | p.Arg304Cys | missense_variant | 6/15 | 1 | NM_004728.4 | ENSP00000346120 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000265 AC: 4AN: 151134Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248476Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134302
GnomAD4 exome AF: 0.0000337 AC: 49AN: 1454564Hom.: 0 Cov.: 30 AF XY: 0.0000346 AC XY: 25AN XY: 723330
GnomAD4 genome AF: 0.0000265 AC: 4AN: 151134Hom.: 0 Cov.: 31 AF XY: 0.0000271 AC XY: 2AN XY: 73666
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 26, 2023 | The c.910C>T (p.R304C) alteration is located in exon 6 (coding exon 6) of the DDX21 gene. This alteration results from a C to T substitution at nucleotide position 910, causing the arginine (R) at amino acid position 304 to be replaced by a cysteine (C). 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