Variant chr9-116440600-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_001365068.1(ASTN2):c.3782+9G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 1,611,472 control chromosomes in the GnomAD database, including 18,231 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.12 ( 1324 hom., cov: 32)

Exomes 𝑓: 0.15 ( 16907 hom. )

Consequence

ASTN2
NM_001365068.1 intron

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -2.23

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]

ASTN2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 9-116440600-C-A is Benign according to our data. Variant chr9-116440600-C-A is described in ClinVar as [Benign]. Clinvar id is 3060454.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASTN2	NM_001365068.1 linkuse as main transcript	c.3782+9G>T		intron_variant		ENST00000313400.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASTN2	ENST00000313400.9 linkuse as main transcript	c.3782+9G>T		intron_variant		5	NM_001365068.1	A2	O75129-1

Frequencies

GnomAD3 genomes

AF:

0.124

AC:

18828

AN:

152096

Hom.:

1327

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0717

Gnomad AMI

AF:

0.227

Gnomad AMR

AF:

0.124

Gnomad ASJ

AF:

0.201

Gnomad EAS

AF:

0.000579

Gnomad SAS

AF:

0.0810

Gnomad FIN

AF:

0.147

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.158

Gnomad OTH

AF:

0.133

GnomAD3 exomes

AF:

0.124

AC:

31058

AN:

250752

Hom.:

2325

AF XY:

0.126

AC XY:

17133

AN XY:

135500

show subpopulations

Gnomad AFR exome

AF:

0.0676

Gnomad AMR exome

AF:

0.0868

Gnomad ASJ exome

AF:

0.202

Gnomad EAS exome

AF:

0.000272

Gnomad SAS exome

AF:

0.0907

Gnomad FIN exome

AF:

0.151

Gnomad NFE exome

AF:

0.159

Gnomad OTH exome

AF:

0.146

GnomAD4 exome

AF:

0.147

AC:

214169

AN:

1459258

Hom.:

16907

Cov.:

AF XY:

0.146

AC XY:

105977

AN XY:

725916

show subpopulations

Gnomad4 AFR exome

AF:

0.0699

Gnomad4 AMR exome

AF:

0.0915

Gnomad4 ASJ exome

AF:

0.204

Gnomad4 EAS exome

AF:

0.000277

Gnomad4 SAS exome

AF:

0.0926

Gnomad4 FIN exome

AF:

0.151

Gnomad4 NFE exome

AF:

0.159

Gnomad4 OTH exome

AF:

0.141

GnomAD4 genome

AF:

0.124

AC:

18814

AN:

152214

Hom.:

1324

Cov.:

AF XY:

0.122

AC XY:

9044

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.0715

Gnomad4 AMR

AF:

0.124

Gnomad4 ASJ

AF:

0.201

Gnomad4 EAS

AF:

0.000580

Gnomad4 SAS

AF:

0.0806

Gnomad4 FIN

AF:

0.147

Gnomad4 NFE

AF:

0.158

Gnomad4 OTH

AF:

0.130

Alfa

AF:

0.135

Hom.:

895

Bravo

AF:

0.120

Asia WGS

AF:

0.0370

AC:

127

AN:

3478

EpiCase

AF:

0.158

EpiControl

AF:

0.166

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ASTN2-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 21, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.015

DANN

Benign

0.37

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over