1-57634035-A-G

Variant names:

• chr1-57634035-A-G
• rs1539053
• NM_001379462.1:c.-137+15557T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001379462.1(DAB1):​c.-137+15557T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 152,080 control chromosomes in the GnomAD database, including 19,230 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 0.49 (19230 hom., cov: 33)
• Consequence: DAB1 NM_001379462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 11 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAB1	NM_001379462.1	c.-137+15557T>C		intron_variant	Intron 4 of 17		NP_001366391.1
DAB1	NM_021080.5	c.-137+15557T>C		intron_variant	Intron 3 of 16		NP_066566.3
DAB1	NM_001379461.1	c.-137+15557T>C		intron_variant	Intron 7 of 20		NP_001366390.1
DAB1	NM_001353980.2	c.-137+15557T>C		intron_variant	Intron 4 of 5		NP_001340909.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAB1	ENST00000485760.5	n.625+15557T>C		intron_variant	Intron 7 of 20	2

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74966 AN: 151962 Hom.: 19225 Cov.: 33

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.493 AC: 74992 AN: 152080 Hom.: 19230 Cov.: 33 AF XY: 0.495 AC XY: 36764 AN XY: 74324

African (AFR) AF: 0.355 AC: 14732 AN: 41484

American (AMR) AF: 0.458 AC: 6991 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1911 AN: 3472

East Asian (EAS) AF: 0.691 AC: 3564 AN: 5160

South Asian (SAS) AF: 0.448 AC: 2160 AN: 4824

European-Finnish (FIN) AF: 0.568 AC: 6000 AN: 10570

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37891 AN: 67972

Other (OTH) AF: 0.503 AC: 1062 AN: 2112

Alfa AF: 0.536 Hom.: 31310

Bravo AF: 0.479

Asia WGS AF: 0.543 AC: 1890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.40
PhyloP100		-0.19
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1539053; hg19: chr1-58099707;