9-117125435-G-T

Position:

• chr9-117125435-G-T

Variant summary

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

The NM_001365068.1(ASTN2):​c.1168+15891C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,064 control chromosomes in the GnomAD database, including 4,195 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 0.23 (4195 hom., cov: 33)
• Consequence: ASTN2 NM_001365068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

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=-0.55).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASTN2	NM_001365068.1	c.1168+15891C>A		intron_variant		ENST00000313400.9	NP_001351997.1
ASTN2	NM_001365069.1	c.1168+15891C>A		intron_variant			NP_001351998.1
ASTN2	NM_014010.5	c.1016-29284C>A		intron_variant			NP_054729.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASTN2	ENST00000313400.9	c.1168+15891C>A		intron_variant		5	NM_001365068.1	ENSP00000314038.4
ASTN2	ENST00000361209.6	c.1016-29284C>A		intron_variant		1		ENSP00000354504.2
ASTN2	ENST00000361477.8	c.1016-29284C>A		intron_variant		5		ENSP00000355116.5
ASTN2	ENST00000373986.7	c.349+15891C>A		intron_variant		2		ENSP00000363098.3

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35266 AN: 151946 Hom.: 4187 Cov.: 33

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.232 AC: 35286 AN: 152064 Hom.: 4195 Cov.: 33 AF XY: 0.233 AC XY: 17299 AN XY: 74336

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.239

Alfa AF: 0.195 Hom.: 702

Bravo AF: 0.229

Asia WGS AF: 0.278 AC: 965 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	4.1
DANN	Benign	0.62

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: rs1572156; hg19: chr9-119887714;