rs4836732

chr9-116504416-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.3356-16916G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,868 control chromosomes in the GnomAD database, including 19,220 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 0.49 (19218 hom., cov: 30)
  • Exomes 𝑓: 0.63 (2 hom.)
• Consequence: ASTN2 NM_001365068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233

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:51175): (ASTN2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASTN2	NM_001365068.1	c.3356-16916G>A		intron_variant		ENST00000313400.9
ASTN2-AS1	NR_033973.1	n.62+72C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASTN2	ENST00000313400.9	c.3356-16916G>A		intron_variant		5	NM_001365068.1	A2
ASTN2-AS1	ENST00000418250.1	n.62+72C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74731 AN: 151742 Hom.: 19208 Cov.: 30

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.485

GnomAD4 exome AF: 0.625 AC: 5 AN: 8 Hom.: 2 AF XY: 0.667 AC XY: 4 AN XY: 6

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.492 AC: 74771 AN: 151860 Hom.: 19218 Cov.: 30 AF XY: 0.499 AC XY: 37033 AN XY: 74222

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.487

Alfa AF: 0.521 Hom.: 28293

Bravo AF: 0.484

Asia WGS AF: 0.543 AC: 1886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.4
Dann	Benign	0.70

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: rs4836732; hg19: chr9-119266695;