rs10889030

chr1-57163028-T-Achr1-57163028-T-G

Variant summary

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

The NM_001365792.1(DAB1):c.68-17599A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 152,056 control chromosomes in the GnomAD database, including 23,283 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 0.54 (23283 hom., cov: 32)
• Consequence: DAB1 NM_001365792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286

Genes affected

DAB1 (HGNC:2661): (DAB adaptor protein 1) The laminar organization of multiple neuronal types in the cerebral cortex is required for normal cognitive function. In mice, the disabled-1 gene plays a central role in brain development, directing the migration of cortical neurons past previously formed neurons to reach their proper layer. This gene is similar to disabled-1, and the protein encoded by this gene is thought to be a signal transducer that interacts with protein kinase pathways to regulate neuronal positioning in the developing brain. [provided by RefSeq, Jan 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAB1	NM_001365792.1	c.68-17599A>T		intron_variant		ENST00000371236.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAB1	ENST00000371236.7	c.68-17599A>T		intron_variant		5	NM_001365792.1	P1

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81378 AN: 151938 Hom.: 23250 Cov.: 32

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.536 AC: 81466 AN: 152056 Hom.: 23283 Cov.: 32 AF XY: 0.530 AC XY: 39365 AN XY: 74334

Gnomad4 AFR AF: 0.739

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.527

Alfa AF: 0.327 Hom.: 732

Bravo AF: 0.536

Asia WGS AF: 0.509 AC: 1769 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.2
Dann	Benign	0.79

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: rs10889030; hg19: chr1-57628701;