chr21-37493131-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PP2PP3BP4_StrongBP6_Very_StrongBS2
The NM_001347721.2(DYRK1A):āc.1039A>Gā(p.Thr347Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00158 in 1,613,524 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_001347721.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00176 AC: 268AN: 152188Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00195 AC: 489AN: 251372Hom.: 1 AF XY: 0.00188 AC XY: 256AN XY: 135842
GnomAD4 exome AF: 0.00156 AC: 2285AN: 1461218Hom.: 5 Cov.: 34 AF XY: 0.00149 AC XY: 1084AN XY: 726876
GnomAD4 genome AF: 0.00176 AC: 268AN: 152306Hom.: 2 Cov.: 32 AF XY: 0.00218 AC XY: 162AN XY: 74466
ClinVar
Submissions by phenotype
DYRK1A-related intellectual disability syndrome Benign:2
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not provided Benign:2
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DYRK1A: BS1, BS2 -
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Inborn genetic diseases Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
DYRK1A-related disorder Benign:1
This variant is classified as 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