rs1202822

chr1-57880535-C-Achr1-57880535-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000457412.6(DAB1-AS1):n.374C>A variant causes a non coding transcript exon 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-AS1 ENST00000457412.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAB1	NM_001353980.2	c.-211+3464G>T		intron_variant
DAB1	NM_001379461.1	c.-211+3464G>T		intron_variant
DAB1	NM_001379462.1	c.-211+3464G>T		intron_variant
DAB1	NM_021080.5	c.-211+3464G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAB1-AS1	ENST00000457412.6	n.374C>A		non_coding_transcript_exon_variant	4/4	5

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19032 AN: 152016 Hom.: 1382 Cov.: 32

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: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.125 AC: 19044 AN: 152134 Hom.: 1382 Cov.: 32 AF XY: 0.124 AC XY: 9206 AN XY: 74370

Gnomad4 AFR AF: 0.0794

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.0900

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.140

Alfa AF: 0.146 Hom.: 3467

Bravo AF: 0.123

Asia WGS AF: 0.185 AC: 643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.0
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1202822; hg19: chr1-58346207;