rs10889030

Variant names:

• chr1-57163028-T-A
• rs10889030
• NM_001365792.1:c.68-17599A>T

Your query was ambiguous. Multiple possible variants found:

• chr1-57163028-T-A
• chr1-57163028-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• spinocerebellar ataxia type 37

  Inheritance: AD Classification: SUPPORTIVE, LIMITED Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DAB1	NM_001365792.1	c.68-17599A>T		intron_variant	Intron 2 of 14	ENST00000371236.7	NP_001352721.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAB1	ENST00000371236.7	c.68-17599A>T		intron_variant	Intron 2 of 14	5	NM_001365792.1	ENSP00000360280.1

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

African (AFR) AF: 0.739 AC: 30643 AN: 41480

American (AMR) AF: 0.376 AC: 5744 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1715 AN: 3472

East Asian (EAS) AF: 0.545 AC: 2801 AN: 5144

South Asian (SAS) AF: 0.491 AC: 2366 AN: 4816

European-Finnish (FIN) AF: 0.459 AC: 4857 AN: 10586

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31698 AN: 67970

Other (OTH) AF: 0.527 AC: 1108 AN: 2104

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
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10889030; hg19: chr1-57628701;