rs10817934

chr9-116787772-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.2396+17860G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,038 control chromosomes in the GnomAD database, including 4,544 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 0.22 (4544 hom., cov: 32)
• Consequence: ASTN2 NM_001365068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASTN2	NM_001365068.1	c.2396+17860G>A		intron_variant		ENST00000313400.9
ASTN2	NM_001365069.1	c.2384+17860G>A		intron_variant
ASTN2	NM_014010.5	c.2243+17860G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASTN2	ENST00000313400.9	c.2396+17860G>A		intron_variant		5	NM_001365068.1	A2
ASTN2	ENST00000361209.6	c.2243+17860G>A		intron_variant		1		P2
ASTN2	ENST00000361477.8	c.2243+17860G>A		intron_variant		5		A2
ASTN2	ENST00000373986.7	c.1565+17860G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34009 AN: 151920 Hom.: 4544 Cov.: 32

Gnomad AFR AF: 0.0740

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.224 AC: 34005 AN: 152038 Hom.: 4544 Cov.: 32 AF XY: 0.223 AC XY: 16581 AN XY: 74308

Gnomad4 AFR AF: 0.0739

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.223

Alfa AF: 0.281 Hom.: 11423

Bravo AF: 0.209

Asia WGS AF: 0.152 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.5
Dann	Benign	0.22

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs10817934; hg19: chr9-119550051;