9-116551938-A-G

Variant names:

• chr9-116551938-A-G
• rs13290997
• NM_001365068.1:c.3356-64438T>C

Variant summary

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

The NM_001365068.1(ASTN2):​c.3356-64438T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 152,026 control chromosomes in the GnomAD database, including 25,980 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 0.58 (25980 hom., cov: 33)
• Consequence: ASTN2 NM_001365068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 7 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-AS1 (HGNC:51175): (ASTN2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 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.3356-64438T>C		intron	N/A	NP_001351997.1
	ASTN2	NM_001365069.1		c.3344-64438T>C		intron	N/A	NP_001351998.1
	ASTN2	NM_014010.5		c.3203-64438T>C		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.3356-64438T>C		intron	N/A	ENSP00000314038.4
	ASTN2	ENST00000361209.6	TSL:1	c.3203-64438T>C		intron	N/A	ENSP00000354504.2
	ASTN2	ENST00000288520.9	TSL:1	c.659-64438T>C		intron	N/A	ENSP00000288520.5

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88093 AN: 151908 Hom.: 25949 Cov.: 33

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.580 AC: 88173 AN: 152026 Hom.: 25980 Cov.: 33 AF XY: 0.579 AC XY: 43016 AN XY: 74306

African (AFR) AF: 0.673 AC: 27907 AN: 41454

American (AMR) AF: 0.498 AC: 7610 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2077 AN: 3470

East Asian (EAS) AF: 0.554 AC: 2862 AN: 5168

South Asian (SAS) AF: 0.644 AC: 3107 AN: 4824

European-Finnish (FIN) AF: 0.490 AC: 5163 AN: 10540

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37528 AN: 67972

Other (OTH) AF: 0.588 AC: 1244 AN: 2114

Alfa AF: 0.568 Hom.: 34588

Bravo AF: 0.582

Asia WGS AF: 0.574 AC: 1999 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.5
DANN	Benign	0.75
PhyloP100		-0.14
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: rs13290997; hg19: chr9-119314217;