chr21-37500748-C-A

Position:

• chr21-37500748-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001347721.2(DYRK1A):​c.1212+4490C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 151,552 control chromosomes in the GnomAD database, including 23,150 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.55 (23150 hom., cov: 31)
• Consequence: DYRK1A NM_001347721.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

Genes affected

DYRK1A (HGNC:3091): (dual specificity tyrosine phosphorylation regulated kinase 1A) This gene encodes a member of the Dual-specificity tyrosine phosphorylation-regulated kinase (DYRK) family. This member contains a nuclear targeting signal sequence, a protein kinase domain, a leucine zipper motif, and a highly conservative 13-consecutive-histidine repeat. It catalyzes its autophosphorylation on serine/threonine and tyrosine residues. It may play a significant role in a signaling pathway regulating cell proliferation and may be involved in brain development. This gene is a homolog of Drosophila mnb (minibrain) gene and rat Dyrk gene. It is localized in the Down syndrome critical region of chromosome 21, and is considered to be a strong candidate gene for learning defects associated with Down syndrome. Alternative splicing of this gene generates several transcript variants differing from each other either in the 5' UTR or in the 3' coding region. These variants encode at least five different isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DYRK1A	NM_001347721.2	c.1212+4490C>A		intron_variant		ENST00000647188.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DYRK1A	ENST00000647188.2	c.1212+4490C>A		intron_variant			NM_001347721.2	P1

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82627 AN: 151432 Hom.: 23117 Cov.: 31

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.542

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.563

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.546 AC: 82715 AN: 151552 Hom.: 23150 Cov.: 31 AF XY: 0.541 AC XY: 40121 AN XY: 74100

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.565

Alfa AF: 0.536 Hom.: 2783

Bravo AF: 0.547

Asia WGS AF: 0.512 AC: 1762 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.94
DANN	Benign	0.35

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs8132976; hg19: chr21-38873051;