9-116823581-G-A

Variant names:

• chr9-116823581-G-A
• rs1326808
• NM_001365068.1:c.2041-2798C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001365068.1(ASTN2):​c.2041-2798C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.794 in 151,928 control chromosomes in the GnomAD database, including 48,070 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 0.79 (48070 hom., cov: 32)
• Consequence: ASTN2 NM_001365068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• autism spectrum disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
• intellectual disability

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001365068.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASTN2	NM_001365068.1	MANE Select	c.2041-2798C>T		intron	N/A	NP_001351997.1
	ASTN2	NM_001365069.1		c.2029-2798C>T		intron	N/A	NP_001351998.1
	ASTN2	NM_014010.5		c.1888-2798C>T		intron	N/A	NP_054729.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASTN2	ENST00000313400.9	TSL:5 MANE Select	c.2041-2798C>T		intron	N/A	ENSP00000314038.4
	ASTN2	ENST00000361209.6	TSL:1	c.1888-2798C>T		intron	N/A	ENSP00000354504.2
	ASTN2	ENST00000361477.8	TSL:5	c.1888-2798C>T		intron	N/A	ENSP00000355116.5

Frequencies

GnomAD3 genomes AF: 0.794 AC: 120527 AN: 151810 Hom.: 48037 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.862

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.920

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.836

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.794 AC: 120617 AN: 151928 Hom.: 48070 Cov.: 32 AF XY: 0.795 AC XY: 59002 AN XY: 74244

African (AFR) AF: 0.750 AC: 31055 AN: 41430

American (AMR) AF: 0.873 AC: 13338 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.862 AC: 2992 AN: 3472

East Asian (EAS) AF: 0.915 AC: 4719 AN: 5156

South Asian (SAS) AF: 0.778 AC: 3741 AN: 4810

European-Finnish (FIN) AF: 0.745 AC: 7855 AN: 10540

Middle Eastern (MID) AF: 0.914 AC: 267 AN: 292

European-Non Finnish (NFE) AF: 0.797 AC: 54124 AN: 67920

Other (OTH) AF: 0.836 AC: 1768 AN: 2116

Alfa AF: 0.790 Hom.: 6165

Bravo AF: 0.805

Asia WGS AF: 0.823 AC: 2863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.30
DANN	Benign	0.52
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1326808; hg19: chr9-119585860;