NM_001365068.1:c.3356-37776T>C

Variant names:

• chr9-116525276-A-G
• rs12237388
• NM_001365068.1:c.3356-37776T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001365068.1(ASTN2):​c.3356-37776T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,222 control chromosomes in the GnomAD database, including 2,565 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 0.18 (2565 hom., cov: 33)
• Consequence: ASTN2 NM_001365068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001365068.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASTN2	NM_001365068.1	MANE Select	c.3356-37776T>C		intron	N/A	NP_001351997.1	O75129-1
	ASTN2	NM_001365069.1		c.3344-37776T>C		intron	N/A	NP_001351998.1	O75129-3
	ASTN2	NM_014010.5		c.3203-37776T>C		intron	N/A	NP_054729.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASTN2	ENST00000313400.9	TSL:5 MANE Select	c.3356-37776T>C		intron	N/A	ENSP00000314038.4	O75129-1
	ASTN2	ENST00000361209.6	TSL:1	c.3203-37776T>C		intron	N/A	ENSP00000354504.2	O75129-2
	ASTN2	ENST00000288520.9	TSL:1	c.659-37776T>C		intron	N/A	ENSP00000288520.5	O75129-4

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27166 AN: 152104 Hom.: 2559 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0988

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.179 AC: 27195 AN: 152222 Hom.: 2565 Cov.: 33 AF XY: 0.178 AC XY: 13283 AN XY: 74420

African (AFR) AF: 0.237 AC: 9856 AN: 41512

American (AMR) AF: 0.151 AC: 2308 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0988 AC: 343 AN: 3472

East Asian (EAS) AF: 0.200 AC: 1033 AN: 5174

South Asian (SAS) AF: 0.153 AC: 737 AN: 4824

European-Finnish (FIN) AF: 0.167 AC: 1772 AN: 10600

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10647 AN: 68020

Other (OTH) AF: 0.165 AC: 349 AN: 2114

Alfa AF: 0.160 Hom.: 8871

Bravo AF: 0.181

Asia WGS AF: 0.201 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.7
DANN	Benign	0.73
PhyloP100		-0.11
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: rs12237388; hg19: chr9-119287555;