rs12376789

Positions:

• chr9-116620855-C-G

Variant summary

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

The NM_001365068.1(ASTN2):​c.3073-412G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,150 control chromosomes in the GnomAD database, including 995 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 0.11 (995 hom., cov: 32)
• Consequence: ASTN2 NM_001365068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113

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]

LOC105376240 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASTN2	NM_001365068.1	c.3073-412G>C		intron_variant		ENST00000313400.9	NP_001351997.1
LOC105376240	XR_930277.3	n.82-6512C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASTN2	ENST00000313400.9	c.3073-412G>C		intron_variant		5	NM_001365068.1	ENSP00000314038	A2

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16723 AN: 152032 Hom.: 990 Cov.: 32

Gnomad AFR AF: 0.0853

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.0887

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.0800

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.0996

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

GnomAD4 genome AF: 0.110 AC: 16738 AN: 152150 Hom.: 995 Cov.: 32 AF XY: 0.109 AC XY: 8074 AN XY: 74392

Gnomad4 AFR AF: 0.0852

Gnomad4 AMR AF: 0.0893

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.0799

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.0995

Alfa AF: 0.130 Hom.: 176

Bravo AF: 0.105

Asia WGS AF: 0.119 AC: 412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.36

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: rs12376789; hg19: chr9-119383134;