19-39825793-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_004714.3(DYRK1B):c.1812G>A(p.Pro604Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,575,366 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars). Synonymous variant affecting the same amino acid position (i.e. P604P) has been classified as Likely benign.
Frequency
Consequence
NM_004714.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DYRK1B | NM_004714.3 | c.1812G>A | p.Pro604Pro | synonymous_variant | Exon 11 of 11 | ENST00000323039.10 | NP_004705.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151938Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000228 AC: 4AN: 175086Hom.: 0 AF XY: 0.0000415 AC XY: 4AN XY: 96302
GnomAD4 exome AF: 0.0000260 AC: 37AN: 1423428Hom.: 0 Cov.: 33 AF XY: 0.0000241 AC XY: 17AN XY: 705416
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151938Hom.: 0 Cov.: 31 AF XY: 0.0000539 AC XY: 4AN XY: 74198
ClinVar
Submissions by phenotype
DYRK1B-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at