GeneBe

1-57880535-C-T

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000457412.6(DAB1-AS1):​n.374C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

DAB1-AS1
ENST00000457412.6 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06

Publications

3 publications found
Variant links:
Genes affected
DAB1-AS1 (HGNC:49443): (DAB1 antisense RNA 1)
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)

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DAB1NM_001379462.1 linkc.-211+3464G>A intron_variant Intron 3 of 17 NP_001366391.1
DAB1NM_021080.5 linkc.-211+3464G>A intron_variant Intron 2 of 16 NP_066566.3 O75553-6
DAB1NM_001379461.1 linkc.-211+3464G>A intron_variant Intron 6 of 20 NP_001366390.1
DAB1NM_001353980.2 linkc.-211+3464G>A intron_variant Intron 3 of 5 NP_001340909.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DAB1-AS1ENST00000457412.6 linkn.374C>T non_coding_transcript_exon_variant Exon 4 of 4 5
DAB1-AS1ENST00000586465.5 linkn.552C>T non_coding_transcript_exon_variant Exon 6 of 6 5
DAB1-AS1ENST00000591173.5 linkn.525C>T non_coding_transcript_exon_variant Exon 5 of 5 5

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
6
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
4
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
4
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
2
Other (OTH)
AC:
0
AN:
0
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
7189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.3
DANN
Benign
0.80
PhyloP100
-1.1

Splicing

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

Publications

Other links and lift over

dbSNP: rs1202822; hg19: chr1-58346207; API