rs1326808
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001365068.1(ASTN2):c.2041-2798C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.794 in 151,928 control chromosomes in the GnomAD database, including 48,070 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 0.79 ( 48070 hom., cov: 32)
Consequence
ASTN2
NM_001365068.1 intron
NM_001365068.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.12
Genes affected
ASTN2 (HGNC:17021): (astrotactin 2) This gene encodes a protein that is expressed in the brain and may function in neuronal migration, based on functional studies of the related astrotactin 1 gene in human and mouse. A deletion at this locus has been associated with schizophrenia. Multiple transcript variants encoding different proteins have been found for this locus. [provided by RefSeq, May 2010]
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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=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ASTN2 | NM_001365068.1 | c.2041-2798C>T | intron_variant | ENST00000313400.9 | NP_001351997.1 | |||
ASTN2 | NM_001365069.1 | c.2029-2798C>T | intron_variant | NP_001351998.1 | ||||
ASTN2 | NM_014010.5 | c.1888-2798C>T | intron_variant | NP_054729.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ASTN2 | ENST00000313400.9 | c.2041-2798C>T | intron_variant | 5 | NM_001365068.1 | ENSP00000314038.4 | ||||
ASTN2 | ENST00000361209.6 | c.1888-2798C>T | intron_variant | 1 | ENSP00000354504.2 | |||||
ASTN2 | ENST00000361477.8 | c.1888-2798C>T | intron_variant | 5 | ENSP00000355116.5 | |||||
ASTN2 | ENST00000373986.7 | c.1210-2798C>T | intron_variant | 2 | ENSP00000363098.3 |
Frequencies
GnomAD3 genomes AF: 0.794 AC: 120527AN: 151810Hom.: 48037 Cov.: 32
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.794 AC: 120617AN: 151928Hom.: 48070 Cov.: 32 AF XY: 0.795 AC XY: 59002AN XY: 74244
GnomAD4 genome
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2863
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3478
ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at