NM_001365068.1:c.1890-48710G>A

Variant names:

• chr9-116912443-C-T
• rs944323
• NM_001365068.1:c.1890-48710G>A

Variant summary

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

The NM_001365068.1(ASTN2):​c.1890-48710G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 152,076 control chromosomes in the GnomAD database, including 21,785 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 0.53 (21785 hom., cov: 33)
• Consequence: ASTN2 NM_001365068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

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=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASTN2	NM_001365068.1	c.1890-48710G>A		intron_variant	Intron 10 of 22	ENST00000313400.9	NP_001351997.1
ASTN2	NM_001365069.1	c.1878-48710G>A		intron_variant	Intron 10 of 22		NP_001351998.1
ASTN2	NM_014010.5	c.1737-48710G>A		intron_variant	Intron 9 of 21		NP_054729.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASTN2	ENST00000313400.9	c.1890-48710G>A		intron_variant	Intron 10 of 22	5	NM_001365068.1	ENSP00000314038.4
ASTN2	ENST00000361209.6	c.1737-48710G>A		intron_variant	Intron 9 of 21	1		ENSP00000354504.2
ASTN2	ENST00000361477.8	c.1737-48710G>A		intron_variant	Intron 9 of 22	5		ENSP00000355116.5
ASTN2	ENST00000373986.7	c.1059-48710G>A		intron_variant	Intron 8 of 20	2		ENSP00000363098.3

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80088 AN: 151958 Hom.: 21765 Cov.: 33

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.527 AC: 80157 AN: 152076 Hom.: 21785 Cov.: 33 AF XY: 0.523 AC XY: 38862 AN XY: 74326

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.524

Alfa AF: 0.574 Hom.: 33376

Bravo AF: 0.520

Asia WGS AF: 0.368 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	13
DANN	Benign	0.77

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: rs944323; hg19: chr9-119674722;