9-117004690-C-T

Position:

• chr9-117004690-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.1591+3402G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 151,980 control chromosomes in the GnomAD database, including 27,173 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 0.56 (27173 hom., cov: 32)
• Consequence: ASTN2 NM_001365068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASTN2	NM_001365068.1	c.1591+3402G>A		intron_variant		ENST00000313400.9	NP_001351997.1
ASTN2	NM_001365069.1	c.1591+3402G>A		intron_variant			NP_001351998.1
ASTN2	NM_014010.5	c.1438+3402G>A		intron_variant			NP_054729.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASTN2	ENST00000313400.9	c.1591+3402G>A		intron_variant		5	NM_001365068.1	ENSP00000314038.4
ASTN2	ENST00000361209.6	c.1438+3402G>A		intron_variant		1		ENSP00000354504.2
ASTN2	ENST00000361477.8	c.1438+3402G>A		intron_variant		5		ENSP00000355116.5
ASTN2	ENST00000373986.7	c.772+3402G>A		intron_variant		2		ENSP00000363098.3

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84783 AN: 151862 Hom.: 27156 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.558 AC: 84819 AN: 151980 Hom.: 27173 Cov.: 32 AF XY: 0.561 AC XY: 41665 AN XY: 74256

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.711

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.596

Alfa AF: 0.678 Hom.: 46780

Bravo AF: 0.552

Asia WGS AF: 0.630 AC: 2192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.81
DANN	Benign	0.52

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: rs7042036; hg19: chr9-119766969;