rs763907769
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBP6_ModerateBP7BS2_Supporting
The NM_001347721.2(DYRK1A):c.1509G>T(p.Ser503=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000414 in 1,450,668 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 (★). Synonymous variant affecting the same amino acid position (i.e. S503S) has been classified as Likely benign.
Frequency
Consequence
NM_001347721.2 synonymous
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 |
---|---|---|---|---|---|---|---|
DYRK1A | NM_001347721.2 | c.1509G>T | p.Ser503= | synonymous_variant | 10/12 | ENST00000647188.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DYRK1A | ENST00000647188.2 | c.1509G>T | p.Ser503= | synonymous_variant | 10/12 | NM_001347721.2 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000827 AC: 2AN: 241926Hom.: 0 AF XY: 0.0000152 AC XY: 2AN XY: 131478
GnomAD4 exome AF: 0.00000414 AC: 6AN: 1450668Hom.: 0 Cov.: 31 AF XY: 0.00000416 AC XY: 3AN XY: 721870
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
DYRK1A-related intellectual disability syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 05, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at