rs11207007

chr1-57327683-C-T

Variant summary

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

The NM_001365792.1(DAB1):c.-136-36517G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,936 control chromosomes in the GnomAD database, including 10,072 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 0.35 (10072 hom., cov: 31)
• Consequence: DAB1 NM_001365792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48

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).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAB1	NM_001365792.1	c.-136-36517G>A		intron_variant		ENST00000371236.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAB1	ENST00000371236.7	c.-136-36517G>A		intron_variant		5	NM_001365792.1	P1
DAB1	ENST00000371230.1	c.-136-36517G>A		intron_variant		5
DAB1	ENST00000485760.5	n.626-36517G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52787 AN: 151818 Hom.: 10074 Cov.: 31

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.348 AC: 52799 AN: 151936 Hom.: 10072 Cov.: 31 AF XY: 0.342 AC XY: 25363 AN XY: 74264

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.363

Alfa AF: 0.379 Hom.: 2051

Bravo AF: 0.343

Asia WGS AF: 0.154 AC: 534 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	0.065
Dann	Benign	0.28

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: rs11207007; hg19: chr1-57793355; COSMIC: COSV64680407;