dbSNP rs1202822: DAB1:c.-211+3464G>T (chr1-57880535-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_021080.5(DAB1):c.-211+3464G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,134 control chromosomes in the GnomAD database, including 1,382 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 0.13 ( 1382 hom., cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

DAB1
NM_021080.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06

Publications

3 publications found

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]

DAB1 links:

DAB1-AS1 (HGNC:49443): (DAB1 antisense RNA 1)

DAB1-AS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021080.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein	UniProt
DAB1	NM_001379462.1	c.-211+3464G>T	intron	N/A	NP_001366391.1	O75553-6
DAB1	NM_021080.5	c.-211+3464G>T	intron	N/A	NP_066566.3
DAB1	NM_001379461.1	c.-211+3464G>T	intron	N/A	NP_001366390.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
DAB1-AS1	ENST00000457412.6	TSL:5	n.374C>A	non_coding_transcript_exon	Exon 4 of 4
DAB1-AS1	ENST00000586465.5	TSL:5	n.552C>A	non_coding_transcript_exon	Exon 6 of 6
DAB1-AS1	ENST00000591173.5	TSL:5	n.525C>A	non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.125

AC:

19032

AN:

152016

Hom.:

1382

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0794

Gnomad AMI

AF:

0.153

Gnomad AMR

AF:

0.101

Gnomad ASJ

AF:

0.199

Gnomad EAS

AF:

0.267

Gnomad SAS

AF:

0.136

Gnomad FIN

AF:

0.0900

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.148

Gnomad OTH

AF:

0.139

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.125

AC:

19044

AN:

152134

Hom.:

1382

Cov.:

AF XY:

0.124

AC XY:

9206

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.0794

AC:

3296

AN:

41498

American (AMR)

AF:

0.101

AC:

1545

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.199

AC:

690

AN:

3472

East Asian (EAS)

AF:

0.268

AC:

1379

AN:

5152

South Asian (SAS)

AF:

0.136

AC:

658

AN:

4822

European-Finnish (FIN)

AF:

0.0900

AC:

954

AN:

10602

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.148

AC:

10046

AN:

67990

Other (OTH)

AF:

0.140

AC:

296

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

825

1649

2474

3298

4123

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

222

444

666

888

1110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.144

Hom.:

7189

Bravo

AF:

0.123

Asia WGS

AF:

0.185

AC:

643

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.0

(source)

DANN

Benign

0.78

PhyloP100

-1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over