rs2050274

Variant names:

• chr9-117033417-T-C
• rs2050274
• NM_001365068.1:c.1423+6402A>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.1423+6402A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,030 control chromosomes in the GnomAD database, including 41,590 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 0.74 (41590 hom., cov: 32)
• Consequence: ASTN2 NM_001365068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.705
• Publications: 2 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASTN2	NM_001365068.1	c.1423+6402A>G		intron_variant	Intron 6 of 22	ENST00000313400.9	NP_001351997.1
ASTN2	NM_001365069.1	c.1423+6402A>G		intron_variant	Intron 6 of 22		NP_001351998.1
ASTN2	NM_014010.5	c.1270+6402A>G		intron_variant	Intron 5 of 21		NP_054729.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASTN2	ENST00000313400.9	c.1423+6402A>G		intron_variant	Intron 6 of 22	5	NM_001365068.1	ENSP00000314038.4
ASTN2	ENST00000361209.6	c.1270+6402A>G		intron_variant	Intron 5 of 21	1		ENSP00000354504.2
ASTN2	ENST00000361477.8	c.1270+6402A>G		intron_variant	Intron 5 of 22	5		ENSP00000355116.5
ASTN2	ENST00000373986.7	c.604+6402A>G		intron_variant	Intron 4 of 20	2		ENSP00000363098.3

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112191 AN: 151912 Hom.: 41543 Cov.: 32

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.739 AC: 112296 AN: 152030 Hom.: 41590 Cov.: 32 AF XY: 0.738 AC XY: 54848 AN XY: 74306

African (AFR) AF: 0.746 AC: 30973 AN: 41492

American (AMR) AF: 0.733 AC: 11160 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2556 AN: 3470

East Asian (EAS) AF: 0.859 AC: 4433 AN: 5162

South Asian (SAS) AF: 0.812 AC: 3921 AN: 4826

European-Finnish (FIN) AF: 0.659 AC: 6963 AN: 10570

Middle Eastern (MID) AF: 0.716 AC: 209 AN: 292

European-Non Finnish (NFE) AF: 0.732 AC: 49720 AN: 67958

Other (OTH) AF: 0.769 AC: 1626 AN: 2114

Alfa AF: 0.723 Hom.: 6449

Bravo AF: 0.744

Asia WGS AF: 0.830 AC: 2884 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.27
DANN	Benign	0.73
PhyloP100		-0.70
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: rs2050274; hg19: chr9-119795696;