rs694060

chr1-57277572-A-T

Variant summary

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

The NM_001365792.1(DAB1):c.67+13392T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 152,006 control chromosomes in the GnomAD database, including 45,668 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 0.77 (45668 hom., cov: 31)
• Consequence: DAB1 NM_001365792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAB1	NM_001365792.1	c.67+13392T>A		intron_variant		ENST00000371236.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAB1	ENST00000371236.7	c.67+13392T>A		intron_variant		5	NM_001365792.1	P1

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116255 AN: 151888 Hom.: 45604 Cov.: 31

Gnomad AFR AF: 0.941

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.766 AC: 116376 AN: 152006 Hom.: 45668 Cov.: 31 AF XY: 0.767 AC XY: 56983 AN XY: 74278

Gnomad4 AFR AF: 0.941

Gnomad4 AMR AF: 0.839

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.774

Alfa AF: 0.739 Hom.: 5256

Bravo AF: 0.787

Asia WGS AF: 0.673 AC: 2343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	1.8
Dann	Benign	0.77

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: rs694060; hg19: chr1-57743244;