19-39825887-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_004714.3(DYRK1B):āc.1718C>Gā(p.Ala573Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000158 in 1,584,572 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_004714.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DYRK1B | NM_004714.3 | c.1718C>G | p.Ala573Gly | missense_variant | 11/11 | ENST00000323039.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DYRK1B | ENST00000323039.10 | c.1718C>G | p.Ala573Gly | missense_variant | 11/11 | 1 | NM_004714.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152006Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000946 AC: 2AN: 211448Hom.: 0 AF XY: 0.00000872 AC XY: 1AN XY: 114688
GnomAD4 exome AF: 0.0000161 AC: 23AN: 1432566Hom.: 0 Cov.: 33 AF XY: 0.0000113 AC XY: 8AN XY: 710138
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152006Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74250
ClinVar
Submissions by phenotype
DYRK1B-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 06, 2024 | The DYRK1B c.1718C>G variant is predicted to result in the amino acid substitution p.Ala573Gly. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0021% of alleles in individuals of European (Non-Finnish) descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at