chr9-116697371-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001365068.1(ASTN2):c.2806+28400T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00499 in 289,224 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0082 ( 21 hom., cov: 32)
Exomes 𝑓: 0.0015 ( 1 hom. )
Consequence
ASTN2
NM_001365068.1 intron
NM_001365068.1 intron
Scores
2
Splicing: ADA: 0.3886
1
1
Clinical Significance
Conservation
PhyloP100: 0.638
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]
TRIM32 (HGNC:16380): (tripartite motif containing 32) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The protein localizes to cytoplasmic bodies. The protein has also been localized to the nucleus, where it interacts with the activation domain of the HIV-1 Tat protein. The Tat protein activates transcription of HIV-1 genes. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
?
Variant 9-116697371-A-G is Benign according to our data. Variant chr9-116697371-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1188514.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00816 (1243/152320) while in subpopulation AFR AF= 0.0289 (1202/41576). AF 95% confidence interval is 0.0276. There are 21 homozygotes in gnomad4. There are 582 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 21 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASTN2 | NM_001365068.1 | c.2806+28400T>C | intron_variant | ENST00000313400.9 | |||
TRIM32 | NM_012210.4 | c.-81-291A>G | intron_variant | ENST00000450136.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASTN2 | ENST00000313400.9 | c.2806+28400T>C | intron_variant | 5 | NM_001365068.1 | A2 | |||
TRIM32 | ENST00000450136.2 | c.-81-291A>G | intron_variant | 1 | NM_012210.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00816 AC: 1242AN: 152202Hom.: 21 Cov.: 32
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GnomAD4 exome AF: 0.00146 AC: 200AN: 136904Hom.: 1 Cov.: 0 AF XY: 0.00124 AC XY: 89AN XY: 72062
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GnomAD4 genome ? AF: 0.00816 AC: 1243AN: 152320Hom.: 21 Cov.: 32 AF XY: 0.00781 AC XY: 582AN XY: 74484
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 02, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at