9-116548086-C-T

Position:

• chr9-116548086-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.3356-60586G>A variant causes a intron change. The variant allele was found at a frequency of 0.173 in 139,776 control chromosomes in the GnomAD database, including 2,089 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 0.17 (2089 hom., cov: 32)
• Consequence: ASTN2 NM_001365068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.82

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:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASTN2	NM_001365068.1	c.3356-60586G>A		intron_variant		ENST00000313400.9	NP_001351997.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASTN2	ENST00000313400.9	c.3356-60586G>A		intron_variant		5	NM_001365068.1	ENSP00000314038.4

Frequencies

GnomAD3 genomes AF: 0.173 AC: 24128 AN: 139658 Hom.: 2080 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0104

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.173 AC: 24154 AN: 139776 Hom.: 2089 Cov.: 32 AF XY: 0.171 AC XY: 11608 AN XY: 67928

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.0104

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.191

Alfa AF: 0.108 Hom.: 235

Bravo AF: 0.163

Asia WGS AF: 0.0530 AC: 185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	20
DANN	Benign	0.75

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: rs4837614; hg19: chr9-119310365;