rs1889318

Variant names:

• chr9-117080772-T-C
• rs1889318
• NM_001365068.1:c.1276+15272A>G

Your query was ambiguous. Multiple possible variants found:

• chr9-117080772-T-C
• chr9-117080772-T-G

Variant summary

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

The NM_001365068.1(ASTN2):​c.1276+15272A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,030 control chromosomes in the GnomAD database, including 8,599 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 0.31 (8599 hom., cov: 32)
• Consequence: ASTN2 NM_001365068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASTN2	NM_001365068.1	c.1276+15272A>G		intron_variant	Intron 5 of 22	ENST00000313400.9	NP_001351997.1
ASTN2	NM_001365069.1	c.1276+15272A>G		intron_variant	Intron 5 of 22		NP_001351998.1
ASTN2	NM_014010.5	c.1123+15272A>G		intron_variant	Intron 4 of 21		NP_054729.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASTN2	ENST00000313400.9	c.1276+15272A>G		intron_variant	Intron 5 of 22	5	NM_001365068.1	ENSP00000314038.4
ASTN2	ENST00000361209.6	c.1123+15272A>G		intron_variant	Intron 4 of 21	1		ENSP00000354504.2
ASTN2	ENST00000361477.8	c.1123+15272A>G		intron_variant	Intron 4 of 22	5		ENSP00000355116.5
ASTN2	ENST00000373986.7	c.457+15272A>G		intron_variant	Intron 3 of 20	2		ENSP00000363098.3

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46637 AN: 151912 Hom.: 8603 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.307 AC: 46629 AN: 152030 Hom.: 8599 Cov.: 32 AF XY: 0.302 AC XY: 22476 AN XY: 74306

African (AFR) AF: 0.113 AC: 4709 AN: 41496

American (AMR) AF: 0.308 AC: 4702 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1405 AN: 3470

East Asian (EAS) AF: 0.119 AC: 612 AN: 5164

South Asian (SAS) AF: 0.277 AC: 1336 AN: 4822

European-Finnish (FIN) AF: 0.371 AC: 3925 AN: 10570

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28724 AN: 67942

Other (OTH) AF: 0.330 AC: 696 AN: 2108

Alfa AF: 0.379 Hom.: 19933

Bravo AF: 0.293

Asia WGS AF: 0.172 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.53
PhyloP100		-0.20
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: rs1889318; hg19: chr9-119843051;