rs4836732

Variant names:

• chr9-116504416-C-T
• rs4836732
• NM_001365068.1:c.3356-16916G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 25 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ASTN2	NM_001365068.1	c.3356-16916G>A		intron_variant	Intron 19 of 22	ENST00000313400.9	NP_001351997.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASTN2	ENST00000313400.9	c.3356-16916G>A		intron_variant	Intron 19 of 22	5	NM_001365068.1	ENSP00000314038.4

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 4 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.339 AC: 14070 AN: 41454

American (AMR) AF: 0.595 AC: 9079 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1721 AN: 3468

East Asian (EAS) AF: 0.578 AC: 2964 AN: 5132

South Asian (SAS) AF: 0.655 AC: 3149 AN: 4804

European-Finnish (FIN) AF: 0.588 AC: 6192 AN: 10524

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.527 AC: 35783 AN: 67920

Other (OTH) AF: 0.487 AC: 1026 AN: 2108

Alfa AF: 0.516 Hom.: 34986

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
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4836732; hg19: chr9-119266695;