rs4110981

Positions:

• chr1-58046377-T-C
• chr1-58046377-T-G

Variant summary

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

The NM_021080.5(DAB1):​c.-374-162215A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 152,010 control chromosomes in the GnomAD database, including 14,769 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 0.43 (14769 hom., cov: 32)
• Consequence: DAB1 NM_021080.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510

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]

DAB1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DAB1	NM_001379462.1	c.-450-75512A>G		intron_variant			NP_001366391.1
DAB1	NM_021080.5	c.-374-162215A>G		intron_variant			NP_066566.3
DAB1	NM_001379461.1	c.-375+104134A>G		intron_variant			NP_001366390.1
DAB1	NM_001353980.2	c.-450-75512A>G		intron_variant			NP_001340909.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DAB1	ENST00000485760.5	n.387+104134A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65549 AN: 151892 Hom.: 14767 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.431 AC: 65570 AN: 152010 Hom.: 14769 Cov.: 32 AF XY: 0.428 AC XY: 31789 AN XY: 74302

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.403

Alfa AF: 0.480 Hom.: 35395

Bravo AF: 0.425

Asia WGS AF: 0.222 AC: 773 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4110981; hg19: chr1-58512049; COSMIC: COSV64717995;