rs6478241

chr9-116490350-A-Gchr9-116490350-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.3356-2850T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 143,168 control chromosomes in the GnomAD database, including 22,872 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 0.55 (22872 hom., cov: 21)
• Consequence: ASTN2 NM_001365068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.745

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASTN2	NM_001365068.1	c.3356-2850T>C		intron_variant		ENST00000313400.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASTN2	ENST00000313400.9	c.3356-2850T>C		intron_variant		5	NM_001365068.1	A2

Frequencies

GnomAD3 genomes AF: 0.547 AC: 78323 AN: 143092 Hom.: 22856 Cov.: 21

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.616

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.547 AC: 78357 AN: 143168 Hom.: 22872 Cov.: 21 AF XY: 0.549 AC XY: 37837 AN XY: 68936

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.557

Alfa AF: 0.621 Hom.: 60891

Bravo AF: 0.539

Asia WGS AF: 0.625 AC: 2171 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	1.4
Dann	Benign	0.68

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: rs6478241; hg19: chr9-119252629;