rs1325445

chr1-58001703-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_021080.5(DAB1):c.-374-117541G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.016 in 152,260 control chromosomes in the GnomAD database, including 30 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 0.016 (30 hom., cov: 32)
• Consequence: DAB1 NM_021080.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340

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=-0.9).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.016 (2440/152260) while in subpopulation SAS AF= 0.0311 (150/4816). AF 95% confidence interval is 0.0271. There are 30 homozygotes in gnomad4. There are 1258 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High AC in GnomAd at 2438 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAB1	NM_001353980.2	c.-450-30838G>A		intron_variant
DAB1	NM_001379461.1	c.-374-117541G>A		intron_variant
DAB1	NM_001379462.1	c.-450-30838G>A		intron_variant
DAB1	NM_021080.5	c.-374-117541G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAB1	ENST00000485760.5	n.388-117541G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0160 AC: 2438 AN: 152142 Hom.: 30 Cov.: 32

Gnomad AFR AF: 0.00365

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0112

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0309

Gnomad FIN AF: 0.0352

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0215

Gnomad OTH AF: 0.0177

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

GnomAD4 genome AF: 0.0160 AC: 2440 AN: 152260 Hom.: 30 Cov.: 32 AF XY: 0.0169 AC XY: 1258 AN XY: 74446

Gnomad4 AFR AF: 0.00364

Gnomad4 AMR AF: 0.0112

Gnomad4 ASJ AF: 0.0199

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0311

Gnomad4 FIN AF: 0.0352

Gnomad4 NFE AF: 0.0215

Gnomad4 OTH AF: 0.0175

Alfa AF: 0.0171 Hom.: 4

Bravo AF: 0.0134

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.71
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1325445; hg19: chr1-58467375;