rs6667588

Variant names:

• chr1-177047232-A-G
• rs6667588
• NM_004319.3:c.471+13846T>C

Variant summary

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

The NM_004319.3(ASTN1):​c.471+13846T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 152,106 control chromosomes in the GnomAD database, including 22,770 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 0.54 (22770 hom., cov: 32)
• Consequence: ASTN1 NM_004319.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 3 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004319.3. 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
	ASTN1	NM_004319.3	MANE Select	c.471+13846T>C		intron	N/A	NP_004310.1	O14525-2
	ASTN1	NM_001364856.2		c.471+13846T>C		intron	N/A	NP_001351785.1	O14525-1
	ASTN1	NM_001286164.2		c.471+13846T>C		intron	N/A	NP_001273093.1	B1AJS1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASTN1	ENST00000361833.7	TSL:1 MANE Select	c.471+13846T>C		intron	N/A	ENSP00000354536.2	O14525-2
	ASTN1	ENST00000367657.7	TSL:1	c.471+13846T>C		intron	N/A	ENSP00000356629.3	B1AJS1
	ASTN1	ENST00000424564.2	TSL:1	c.471+13846T>C		intron	N/A	ENSP00000395041.2	O14525-3

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82214 AN: 151986 Hom.: 22747 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.541 AC: 82278 AN: 152106 Hom.: 22770 Cov.: 32 AF XY: 0.535 AC XY: 39791 AN XY: 74342

African (AFR) AF: 0.598 AC: 24808 AN: 41504

American (AMR) AF: 0.490 AC: 7505 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2230 AN: 3466

East Asian (EAS) AF: 0.217 AC: 1123 AN: 5172

South Asian (SAS) AF: 0.405 AC: 1948 AN: 4814

European-Finnish (FIN) AF: 0.537 AC: 5663 AN: 10552

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37357 AN: 67984

Other (OTH) AF: 0.523 AC: 1103 AN: 2108

Alfa AF: 0.546 Hom.: 33371

Bravo AF: 0.541

Asia WGS AF: 0.336 AC: 1176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.084
DANN	Benign	0.36
PhyloP100		-1.5
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: rs6667588; hg19: chr1-177016368;