chr9-117162816-G-T

Position:

• chr9-117162816-G-T

Variant summary

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

The NM_001365068.1(ASTN2):​c.1016-21338C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 151,892 control chromosomes in the GnomAD database, including 6,783 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 0.29 (6783 hom., cov: 32)
• Consequence: ASTN2 NM_001365068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASTN2	NM_001365068.1	c.1016-21338C>A		intron_variant		ENST00000313400.9	NP_001351997.1
ASTN2	NM_001365069.1	c.1016-21338C>A		intron_variant			NP_001351998.1
ASTN2	NM_014010.5	c.1015+51542C>A		intron_variant			NP_054729.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASTN2	ENST00000313400.9	c.1016-21338C>A		intron_variant		5	NM_001365068.1	ENSP00000314038	A2
ASTN2	ENST00000361209.6	c.1015+51542C>A		intron_variant		1		ENSP00000354504	P2
ASTN2	ENST00000361477.8	c.1015+51542C>A		intron_variant		5		ENSP00000355116	A2
ASTN2	ENST00000373986.7	c.197-21338C>A		intron_variant		2		ENSP00000363098

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44744 AN: 151774 Hom.: 6774 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.295 AC: 44786 AN: 151892 Hom.: 6783 Cov.: 32 AF XY: 0.298 AC XY: 22140 AN XY: 74244

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.261

Alfa AF: 0.268 Hom.: 10848

Bravo AF: 0.288

Asia WGS AF: 0.273 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.6
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: rs6478282; hg19: chr9-119925095;