9-116890218-C-T

Position:

• chr9-116890218-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001365068.1(ASTN2):​c.1890-26485G>A variant causes a intron change. The variant allele was found at a frequency of 0.117 in 152,166 control chromosomes in the GnomAD database, including 1,395 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 0.12 (1395 hom., cov: 32)
• Consequence: ASTN2 NM_001365068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.60

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASTN2	NM_001365068.1	c.1890-26485G>A		intron_variant		ENST00000313400.9
ASTN2	NM_001365069.1	c.1878-26485G>A		intron_variant
ASTN2	NM_014010.5	c.1737-26485G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASTN2	ENST00000313400.9	c.1890-26485G>A		intron_variant		5	NM_001365068.1	A2
ASTN2	ENST00000361209.6	c.1737-26485G>A		intron_variant		1		P2
ASTN2	ENST00000361477.8	c.1737-26485G>A		intron_variant		5		A2
ASTN2	ENST00000373986.7	c.1059-26485G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17742 AN: 152048 Hom.: 1396 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.0702

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0583

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0699

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.117 AC: 17755 AN: 152166 Hom.: 1395 Cov.: 32 AF XY: 0.121 AC XY: 8969 AN XY: 74384

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.0702

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0583

Gnomad4 NFE AF: 0.0698

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0948 Hom.: 275

Bravo AF: 0.128

Asia WGS AF: 0.240 AC: 833 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	22
DANN	Benign	0.68

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: rs7035794; hg19: chr9-119652497;