rs11788366

Positions:

• chr9-116500349-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001365068.1(ASTN2):​c.3356-12849C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0425 in 152,258 control chromosomes in the GnomAD database, including 221 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 0.043 (221 hom., cov: 33)
• Consequence: ASTN2 NM_001365068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.767

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASTN2	NM_001365068.1	c.3356-12849C>T		intron_variant		ENST00000313400.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASTN2	ENST00000313400.9	c.3356-12849C>T		intron_variant		5	NM_001365068.1	A2

Frequencies

GnomAD3 genomes AF: 0.0426 AC: 6478 AN: 152140 Hom.: 220 Cov.: 33

Gnomad AFR AF: 0.0113

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0329

Gnomad ASJ AF: 0.0332

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0433

Gnomad FIN AF: 0.0526

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0667

Gnomad OTH AF: 0.0325

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

GnomAD4 genome AF: 0.0425 AC: 6478 AN: 152258 Hom.: 221 Cov.: 33 AF XY: 0.0406 AC XY: 3021 AN XY: 74446

Gnomad4 AFR AF: 0.0113

Gnomad4 AMR AF: 0.0328

Gnomad4 ASJ AF: 0.0332

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0433

Gnomad4 FIN AF: 0.0526

Gnomad4 NFE AF: 0.0667

Gnomad4 OTH AF: 0.0322

Alfa AF: 0.0614 Hom.: 160

Bravo AF: 0.0395

Asia WGS AF: 0.0170 AC: 60 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.6
DANN	Benign	0.58

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

Other links and lift over

dbSNP: rs11788366; hg19: chr9-119262628;