9-116967664-C-T

Position:

• chr9-116967664-C-T

Variant summary

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

The NM_001365068.1(ASTN2):​c.1889+7544G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,078 control chromosomes in the GnomAD database, including 5,688 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 0.27 (5688 hom., cov: 32)
• Consequence: ASTN2 NM_001365068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASTN2	NM_001365068.1	c.1889+7544G>A		intron_variant		ENST00000313400.9
ASTN2	NM_001365069.1	c.1877+7544G>A		intron_variant
ASTN2	NM_014010.5	c.1736+7544G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASTN2	ENST00000313400.9	c.1889+7544G>A		intron_variant		5	NM_001365068.1	A2
ASTN2	ENST00000361209.6	c.1736+7544G>A		intron_variant		1		P2
ASTN2	ENST00000361477.8	c.1736+7544G>A		intron_variant		5		A2
ASTN2	ENST00000373986.7	c.1058+7544G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40615 AN: 151960 Hom.: 5677 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.267 AC: 40652 AN: 152078 Hom.: 5688 Cov.: 32 AF XY: 0.268 AC XY: 19892 AN XY: 74322

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.293

Alfa AF: 0.198 Hom.: 618

Bravo AF: 0.277

Asia WGS AF: 0.227 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.74

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: rs1928980; hg19: chr9-119729943;