rs1016730

chr9-117225050-A-T

Variant summary

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

The NM_001365068.1(ASTN2):c.631-10308T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 152,026 control chromosomes in the GnomAD database, including 23,283 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 0.54 (23283 hom., cov: 32)
• Consequence: ASTN2 NM_001365068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

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]

LOC105376237 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASTN2	NM_001365068.1	c.631-10308T>A		intron_variant		ENST00000313400.9
LOC105376237	XR_930273.3	n.72+6504A>T		intron_variant, non_coding_transcript_variant
ASTN2	NM_001365069.1	c.631-10308T>A		intron_variant
ASTN2	NM_014010.5	c.631-10308T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASTN2	ENST00000313400.9	c.631-10308T>A		intron_variant		5	NM_001365068.1	A2
ASTN2	ENST00000361209.6	c.631-10308T>A		intron_variant		1		P2
ASTN2	ENST00000361477.8	c.631-10308T>A		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82491 AN: 151908 Hom.: 23270 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.543 AC: 82524 AN: 152026 Hom.: 23283 Cov.: 32 AF XY: 0.544 AC XY: 40445 AN XY: 74294

Gnomad4 AFR AF: 0.404

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.859

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.566

Alfa AF: 0.555 Hom.: 2951

Bravo AF: 0.549

Asia WGS AF: 0.720 AC: 2502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.1
Dann	Benign	0.81

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: rs1016730; hg19: chr9-119987329;