1-177160901-C-T

Variant names:

• chr1-177160901-C-T
• rs2014384
• NM_004319.3:c.283+3493G>A

Variant summary

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

The NM_004319.3(ASTN1):​c.283+3493G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,118 control chromosomes in the GnomAD database, including 1,210 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 0.11 (1210 hom., cov: 33)
• Consequence: ASTN1 NM_004319.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• Publications: 5 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASTN1	NM_004319.3	c.283+3493G>A		intron_variant	Intron 1 of 22	ENST00000361833.7	NP_004310.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASTN1	ENST00000361833.7	c.283+3493G>A		intron_variant	Intron 1 of 22	1	NM_004319.3	ENSP00000354536.2

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16897 AN: 152000 Hom.: 1203 Cov.: 33

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0927

Gnomad ASJ AF: 0.0464

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.0543

Gnomad FIN AF: 0.0660

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0812

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.111 AC: 16939 AN: 152118 Hom.: 1210 Cov.: 33 AF XY: 0.107 AC XY: 7966 AN XY: 74364

African (AFR) AF: 0.205 AC: 8492 AN: 41458

American (AMR) AF: 0.0926 AC: 1417 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0464 AC: 161 AN: 3468

East Asian (EAS) AF: 0.0116 AC: 60 AN: 5176

South Asian (SAS) AF: 0.0539 AC: 260 AN: 4822

European-Finnish (FIN) AF: 0.0660 AC: 698 AN: 10582

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0811 AC: 5517 AN: 67988

Other (OTH) AF: 0.103 AC: 218 AN: 2116

Alfa AF: 0.0762 Hom.: 265

Bravo AF: 0.119

Asia WGS AF: 0.0520 AC: 181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.34
PhyloP100		-0.28
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: rs2014384; hg19: chr1-177130037;