9-116548086-C-T

Variant names:

• chr9-116548086-C-T
• rs4837614
• NM_001365068.1:c.3356-60586G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001365068.1(ASTN2):​c.3356-60586G>A variant causes a intron change. The variant allele was found at a frequency of 0.173 in 139,776 control chromosomes in the GnomAD database, including 2,089 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 0.17 (2089 hom., cov: 32)
• Consequence: ASTN2 NM_001365068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.82
• Publications: 0 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 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.3356-60586G>A		intron	N/A	NP_001351997.1	O75129-1
	ASTN2	NM_001365069.1		c.3344-60586G>A		intron	N/A	NP_001351998.1	O75129-3
	ASTN2	NM_014010.5		c.3203-60586G>A		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.3356-60586G>A		intron	N/A	ENSP00000314038.4	O75129-1
	ASTN2	ENST00000361209.6	TSL:1	c.3203-60586G>A		intron	N/A	ENSP00000354504.2	O75129-2
	ASTN2	ENST00000288520.9	TSL:1	c.659-60586G>A		intron	N/A	ENSP00000288520.5	O75129-4

Frequencies

GnomAD3 genomes AF: 0.173 AC: 24128 AN: 139658 Hom.: 2080 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0104

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.173 AC: 24154 AN: 139776 Hom.: 2089 Cov.: 32 AF XY: 0.171 AC XY: 11608 AN XY: 67928

African (AFR) AF: 0.236 AC: 8701 AN: 36908

American (AMR) AF: 0.152 AC: 2171 AN: 14258

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 713 AN: 3316

East Asian (EAS) AF: 0.0104 AC: 46 AN: 4426

South Asian (SAS) AF: 0.109 AC: 413 AN: 3790

European-Finnish (FIN) AF: 0.142 AC: 1413 AN: 9934

Middle Eastern (MID) AF: 0.214 AC: 59 AN: 276

European-Non Finnish (NFE) AF: 0.156 AC: 10020 AN: 64078

Other (OTH) AF: 0.191 AC: 363 AN: 1902

Alfa AF: 0.111 Hom.: 245

Bravo AF: 0.163

Asia WGS AF: 0.0530 AC: 185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	20
DANN	Benign	0.75
PhyloP100		4.8
Mutation Taster		=96/4	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: rs4837614; hg19: chr9-119310365;