rs10489305

Positions:

• chr1-176997688-C-T

Variant summary

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

The NM_004319.3(ASTN1):​c.1523+17103G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 151,676 control chromosomes in the GnomAD database, including 9,959 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 0.35 (9959 hom., cov: 30)
• Consequence: ASTN1 NM_004319.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

Genes affected

ASTN1 (HGNC:773): (astrotactin 1) Astrotactin is a neuronal adhesion molecule required for glial-guided migration of young postmitotic neuroblasts in cortical regions of developing brain, including cerebrum, hippocampus, cerebellum, and olfactory bulb (Fink et al., 1995).[supplied by OMIM, Jun 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASTN1	NM_004319.3	c.1523+17103G>A		intron_variant		ENST00000361833.7	NP_004310.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASTN1	ENST00000361833.7	c.1523+17103G>A		intron_variant		1	NM_004319.3	ENSP00000354536	P1

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52695 AN: 151556 Hom.: 9960 Cov.: 30

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.00737

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.347 AC: 52703 AN: 151676 Hom.: 9959 Cov.: 30 AF XY: 0.341 AC XY: 25244 AN XY: 74102

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.00758

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.348

Alfa AF: 0.380 Hom.: 1717

Bravo AF: 0.334

Asia WGS AF: 0.130 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.6
DANN	Benign	0.81

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: rs10489305; hg19: chr1-176966824;