rs777270510
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 1P and 17B. PP2BP4_StrongBP6_Very_StrongBS1BS2_Supporting
The NM_001347721.2(DYRK1A):āc.1178C>Gā(p.Thr393Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000155 in 1,613,800 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T393A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001347721.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DYRK1A | NM_001347721.2 | c.1178C>G | p.Thr393Ser | missense_variant | 9/12 | ENST00000647188.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DYRK1A | ENST00000647188.2 | c.1178C>G | p.Thr393Ser | missense_variant | 9/12 | NM_001347721.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000996 AC: 25AN: 251006Hom.: 0 AF XY: 0.0000884 AC XY: 12AN XY: 135682
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461618Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727110
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74334
ClinVar
Submissions by phenotype
DYRK1A-related intellectual disability syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 14, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | DYRK1A: PP2, BS1 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at