Variant 9-116687467-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001365068.1(ASTN2):c.2807-35674G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0838 in 143,324 control chromosomes in the GnomAD database, including 526 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.084 ( 487 hom., cov: 21)

Exomes 𝑓: 0.080 ( 39 hom. )

Consequence

ASTN2
NM_001365068.1 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.68

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:

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]

TRIM32 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 9-116687467-C-T is Benign according to our data. Variant chr9-116687467-C-T is described in ClinVar as [Benign]. Clinvar id is 1220919.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASTN2	NM_001365068.1 linkuse as main transcript	c.2807-35674G>A		intron_variant		ENST00000313400.9	NP_001351997.1
TRIM32	NM_012210.4 linkuse as main transcript	c.-82+86C>T		intron_variant		ENST00000450136.2	NP_036342.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASTN2	ENST00000313400.9 linkuse as main transcript	c.2807-35674G>A		intron_variant		5	NM_001365068.1	ENSP00000314038	A2	O75129-1
TRIM32	ENST00000450136.2 linkuse as main transcript	c.-82+86C>T		intron_variant		1	NM_012210.4	ENSP00000408292	P1

Frequencies

GnomAD3 genomes

AF:

0.0841

AC:

11173

AN:

132792

Hom.:

485

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0497

Gnomad AMI

AF:

0.102

Gnomad AMR

AF:

0.0865

Gnomad ASJ

AF:

0.0609

Gnomad EAS

AF:

0.155

Gnomad SAS

AF:

0.110

Gnomad FIN

AF:

0.164

Gnomad MID

AF:

0.0731

Gnomad NFE

AF:

0.0891

Gnomad OTH

AF:

0.0797

GnomAD4 exome

AF:

0.0805

AC:

841

AN:

10448

Hom.:

AF XY:

0.0799

AC XY:

403

AN XY:

5046

show subpopulations

Gnomad4 AFR exome

AF:

0.0529

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.0577

Gnomad4 EAS exome

AF:

0.115

Gnomad4 SAS exome

AF:

0.0885

Gnomad4 NFE exome

AF:

0.0804

Gnomad4 OTH exome

AF:

0.101

GnomAD4 genome

AF:

0.0841

AC:

11174

AN:

132876

Hom.:

487

Cov.:

AF XY:

0.0871

AC XY:

5507

AN XY:

63244

show subpopulations

Gnomad4 AFR

AF:

0.0498

Gnomad4 AMR

AF:

0.0864

Gnomad4 ASJ

AF:

0.0609

Gnomad4 EAS

AF:

0.154

Gnomad4 SAS

AF:

0.109

Gnomad4 FIN

AF:

0.164

Gnomad4 NFE

AF:

0.0891

Gnomad4 OTH

AF:

0.0798

Alfa

AF:

0.0369

Hom.:

Bravo

AF:

0.0768

Asia WGS

AF:

0.140

AC:

485

AN:

3468

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Apr 11, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.17

DANN

Benign

0.91

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