rs1202822

Variant names:

• chr1-57880535-C-A
• rs1202822
• ENST00000457412.6:n.374C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-57880535-C-A
• chr1-57880535-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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)

ACMG classification

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAB1	NM_001379462.1	c.-211+3464G>T		intron_variant	Intron 3 of 17		NP_001366391.1
DAB1	NM_021080.5	c.-211+3464G>T		intron_variant	Intron 2 of 16		NP_066566.3
DAB1	NM_001379461.1	c.-211+3464G>T		intron_variant	Intron 6 of 20		NP_001366390.1
DAB1	NM_001353980.2	c.-211+3464G>T		intron_variant	Intron 3 of 5		NP_001340909.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAB1-AS1	ENST00000457412.6	n.374C>A		non_coding_transcript_exon_variant	Exon 4 of 4	5
DAB1-AS1	ENST00000586465.5	n.552C>A		non_coding_transcript_exon_variant	Exon 6 of 6	5
DAB1-AS1	ENST00000591173.5	n.525C>A		non_coding_transcript_exon_variant	Exon 5 of 5	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

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

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: 41 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10046 AN: 67990

Other (OTH) AF: 0.140 AC: 296 AN: 2114

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.78
PhyloP100		-1.1
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: rs1202822; hg19: chr1-58346207;