chr9-117360523-G-A

Variant names:

• chr9-117360523-G-A
• rs7029526
• NM_001365068.1:c.442+53974C>T

Variant summary

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

The NM_001365068.1(ASTN2):​c.442+53974C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,034 control chromosomes in the GnomAD database, including 8,882 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 0.34 (8882 hom., cov: 32)
• Consequence: ASTN2 NM_001365068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.570

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASTN2	NM_001365068.1	c.442+53974C>T		intron_variant	Intron 1 of 22	ENST00000313400.9	NP_001351997.1
ASTN2	NM_001365069.1	c.442+53974C>T		intron_variant	Intron 1 of 22		NP_001351998.1
ASTN2	NM_014010.5	c.442+53974C>T		intron_variant	Intron 1 of 21		NP_054729.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASTN2	ENST00000313400.9	c.442+53974C>T		intron_variant	Intron 1 of 22	5	NM_001365068.1	ENSP00000314038.4
ASTN2	ENST00000361209.6	c.442+53974C>T		intron_variant	Intron 1 of 21	1		ENSP00000354504.2
ASTN2	ENST00000361477.8	c.442+53974C>T		intron_variant	Intron 1 of 22	5		ENSP00000355116.5

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51106 AN: 151916 Hom.: 8890 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.0520

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.336 AC: 51102 AN: 152034 Hom.: 8882 Cov.: 32 AF XY: 0.335 AC XY: 24880 AN XY: 74312

African (AFR) AF: 0.353 AC: 14633 AN: 41438

American (AMR) AF: 0.284 AC: 4338 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1276 AN: 3466

East Asian (EAS) AF: 0.0517 AC: 267 AN: 5162

South Asian (SAS) AF: 0.247 AC: 1190 AN: 4822

European-Finnish (FIN) AF: 0.354 AC: 3744 AN: 10590

Middle Eastern (MID) AF: 0.383 AC: 111 AN: 290

European-Non Finnish (NFE) AF: 0.361 AC: 24564 AN: 67960

Other (OTH) AF: 0.311 AC: 656 AN: 2108

Alfa AF: 0.350 Hom.: 30352

Bravo AF: 0.328

Asia WGS AF: 0.144 AC: 504 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.68
PhyloP100		0.57
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

Publications

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Other links and lift over

dbSNP: rs7029526; hg19: chr9-120122802;