chr1-57311710-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001365792.1(DAB1):​c.-136-20544A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 151,978 control chromosomes in the GnomAD database, including 22,347 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 ( 22347 hom., cov: 32)

Consequence

DAB1
NM_001365792.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.173
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DAB1NM_001365792.1 linkuse as main transcriptc.-136-20544A>C intron_variant ENST00000371236.7 NP_001352721.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DAB1ENST00000371236.7 linkuse as main transcriptc.-136-20544A>C intron_variant 5 NM_001365792.1 ENSP00000360280.1 O75553-6
DAB1ENST00000371230.1 linkuse as main transcriptc.-136-20544A>C intron_variant 5 ENSP00000360274.1 O75553-2
DAB1ENST00000485760.5 linkuse as main transcriptn.626-20544A>C intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.535
AC:
81241
AN:
151860
Hom.:
22308
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.619
Gnomad AMI
AF:
0.416
Gnomad AMR
AF:
0.661
Gnomad ASJ
AF:
0.493
Gnomad EAS
AF:
0.531
Gnomad SAS
AF:
0.469
Gnomad FIN
AF:
0.449
Gnomad MID
AF:
0.566
Gnomad NFE
AF:
0.477
Gnomad OTH
AF:
0.545
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.535
AC:
81339
AN:
151978
Hom.:
22347
Cov.:
32
AF XY:
0.536
AC XY:
39840
AN XY:
74300
show subpopulations
Gnomad4 AFR
AF:
0.619
Gnomad4 AMR
AF:
0.662
Gnomad4 ASJ
AF:
0.493
Gnomad4 EAS
AF:
0.531
Gnomad4 SAS
AF:
0.469
Gnomad4 FIN
AF:
0.449
Gnomad4 NFE
AF:
0.477
Gnomad4 OTH
AF:
0.544
Alfa
AF:
0.515
Hom.:
4504
Bravo
AF:
0.559
Asia WGS
AF:
0.498
AC:
1732
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
4.8
DANN
Benign
0.76

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs632935; hg19: chr1-57777382; API