rs6478300

Variant names:

• chr9-117273490-C-A
• rs6478300
• NM_001365068.1:c.630+17836G>T

Your query was ambiguous. Multiple possible variants found:

• chr9-117273490-C-A
• chr9-117273490-C-G
• chr9-117273490-C-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.630+17836G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 151,944 control chromosomes in the GnomAD database, including 11,785 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 0.36 (11785 hom., cov: 32)
• Consequence: ASTN2 NM_001365068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• 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 (AFR) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASTN2	NM_001365068.1	c.630+17836G>T		intron_variant	Intron 2 of 22	ENST00000313400.9	NP_001351997.1
ASTN2	NM_001365069.1	c.630+17836G>T		intron_variant	Intron 2 of 22		NP_001351998.1
ASTN2	NM_014010.5	c.630+17836G>T		intron_variant	Intron 2 of 21		NP_054729.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASTN2	ENST00000313400.9	c.630+17836G>T		intron_variant	Intron 2 of 22	5	NM_001365068.1	ENSP00000314038.4
ASTN2	ENST00000361209.6	c.630+17836G>T		intron_variant	Intron 2 of 21	1		ENSP00000354504.2
ASTN2	ENST00000361477.8	c.630+17836G>T		intron_variant	Intron 2 of 22	5		ENSP00000355116.5

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54867 AN: 151826 Hom.: 11763 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.362 AC: 54934 AN: 151944 Hom.: 11785 Cov.: 32 AF XY: 0.363 AC XY: 26946 AN XY: 74280

African (AFR) AF: 0.601 AC: 24878 AN: 41392

American (AMR) AF: 0.271 AC: 4145 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1234 AN: 3466

East Asian (EAS) AF: 0.405 AC: 2085 AN: 5154

South Asian (SAS) AF: 0.445 AC: 2145 AN: 4818

European-Finnish (FIN) AF: 0.256 AC: 2706 AN: 10560

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.245 AC: 16678 AN: 67962

Other (OTH) AF: 0.350 AC: 739 AN: 2110

Alfa AF: 0.285 Hom.: 29449

Bravo AF: 0.370

Asia WGS AF: 0.422 AC: 1471 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	0.48
DANN	Benign	0.34
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs6478300; hg19: chr9-120035769;