9-116722249-C-T
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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.2806+3522G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 151,268 control chromosomes in the GnomAD database, including 14,236 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 0.42 ( 14236 hom., cov: 33)
Consequence
ASTN2
NM_001365068.1 intron
NM_001365068.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.247
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=-0.93).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASTN2 | NM_001365068.1 | c.2806+3522G>A | intron_variant | ENST00000313400.9 | |||
ASTN2 | NM_001365069.1 | c.2794+3522G>A | intron_variant | ||||
ASTN2 | NM_014010.5 | c.2653+3522G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASTN2 | ENST00000313400.9 | c.2806+3522G>A | intron_variant | 5 | NM_001365068.1 | A2 | |||
ASTN2 | ENST00000361209.6 | c.2653+3522G>A | intron_variant | 1 | P2 | ||||
ASTN2 | ENST00000361477.8 | c.2653+3522G>A | intron_variant | 5 | A2 | ||||
ASTN2 | ENST00000373986.7 | c.1975+3522G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.424 AC: 64149AN: 151154Hom.: 14232 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.424 AC: 64187AN: 151268Hom.: 14236 Cov.: 33 AF XY: 0.426 AC XY: 31489AN XY: 73928
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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