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GeneBe

9-116426027-G-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_001365068.1(ASTN2):c.3844C>A(p.Arg1282=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0035 in 1,614,008 control chromosomes in the GnomAD database, including 162 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.019 ( 87 hom., cov: 32)
Exomes 𝑓: 0.0019 ( 75 hom. )

Consequence

ASTN2
NM_001365068.1 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.94
Variant links:
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 -13 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 9-116426027-G-T is Benign according to our data. Variant chr9-116426027-G-T is described in ClinVar as [Benign]. Clinvar id is 792133.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=1.94 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0631 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ASTN2NM_001365068.1 linkuse as main transcriptc.3844C>A p.Arg1282= synonymous_variant 23/23 ENST00000313400.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ASTN2ENST00000313400.9 linkuse as main transcriptc.3844C>A p.Arg1282= synonymous_variant 23/235 NM_001365068.1 A2O75129-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0185
AC:
2819
AN:
152156
Hom.:
84
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0649
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00589
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.0000942
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000191
Gnomad OTH
AF:
0.0134
GnomAD3 exomes
AF:
0.00482
AC:
1205
AN:
249858
Hom.:
36
AF XY:
0.00355
AC XY:
479
AN XY:
135068
show subpopulations
Gnomad AFR exome
AF:
0.0657
Gnomad AMR exome
AF:
0.00289
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000980
Gnomad FIN exome
AF:
0.0000465
Gnomad NFE exome
AF:
0.000187
Gnomad OTH exome
AF:
0.00213
GnomAD4 exome
AF:
0.00192
AC:
2805
AN:
1461734
Hom.:
75
Cov.:
35
AF XY:
0.00163
AC XY:
1185
AN XY:
727166
show subpopulations
Gnomad4 AFR exome
AF:
0.0673
Gnomad4 AMR exome
AF:
0.00340
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000139
Gnomad4 FIN exome
AF:
0.000113
Gnomad4 NFE exome
AF:
0.0000971
Gnomad4 OTH exome
AF:
0.00419
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0186
AC:
2838
AN:
152274
Hom.:
87
Cov.:
32
AF XY:
0.0184
AC XY:
1374
AN XY:
74472
show subpopulations
Gnomad4 AFR
AF:
0.0651
Gnomad4 AMR
AF:
0.00588
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.0000942
Gnomad4 NFE
AF:
0.000191
Gnomad4 OTH
AF:
0.0133
Alfa
AF:
0.00623
Hom.:
8
Bravo
AF:
0.0213
Asia WGS
AF:
0.00722
AC:
26
AN:
3478
EpiCase
AF:
0.000218
EpiControl
AF:
0.000178

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.43
Cadd
Benign
5.3
Dann
Benign
0.59

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs73520334; hg19: chr9-119188306; API