rs6678480

Variant names:

• chr1-177085635-A-C
• rs6678480
• NM_004319.3:c.284-24370T>G

Your query was ambiguous. Multiple possible variants found:

• chr1-177085635-A-C
• chr1-177085635-A-T

Variant summary

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

The NM_004319.3(ASTN1):​c.284-24370T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,990 control chromosomes in the GnomAD database, including 11,479 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 0.36 (11479 hom., cov: 31)
• Consequence: ASTN1 NM_004319.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.568
• Publications: 4 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.482 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.284-24370T>G		intron	N/A	NP_004310.1	O14525-2
	ASTN1	NM_001364856.2		c.284-24370T>G		intron	N/A	NP_001351785.1	O14525-1
	ASTN1	NM_001286164.2		c.284-24370T>G		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.284-24370T>G		intron	N/A	ENSP00000354536.2	O14525-2
	ASTN1	ENST00000367657.7	TSL:1	c.284-24370T>G		intron	N/A	ENSP00000356629.3	B1AJS1
	ASTN1	ENST00000424564.2	TSL:1	c.284-24370T>G		intron	N/A	ENSP00000395041.2	O14525-3

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54686 AN: 151872 Hom.: 11476 Cov.: 31

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.360 AC: 54701 AN: 151990 Hom.: 11479 Cov.: 31 AF XY: 0.354 AC XY: 26296 AN XY: 74284

African (AFR) AF: 0.193 AC: 8003 AN: 41468

American (AMR) AF: 0.286 AC: 4365 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1661 AN: 3464

East Asian (EAS) AF: 0.0138 AC: 71 AN: 5156

South Asian (SAS) AF: 0.230 AC: 1107 AN: 4810

European-Finnish (FIN) AF: 0.498 AC: 5251 AN: 10554

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.486 AC: 33031 AN: 67950

Other (OTH) AF: 0.348 AC: 734 AN: 2112

Alfa AF: 0.426 Hom.: 45160

Bravo AF: 0.335

Asia WGS AF: 0.111 AC: 388 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.5
DANN	Benign	0.63
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

Other links and lift over

dbSNP: rs6678480; hg19: chr1-177054771;