Variant 9-117008201-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001365068.1(ASTN2):c.1482G>A(p.Pro494Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 1,609,010 control chromosomes in the GnomAD database, including 255,371 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.47 ( 19425 hom., cov: 32)

Exomes 𝑓: 0.56 ( 235946 hom. )

Consequence

ASTN2
NM_001365068.1 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.892

Variant links:

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]

ASTN2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP6

Variant 9-117008201-C-T is Benign according to our data. Variant chr9-117008201-C-T is described in ClinVar as [Benign]. Clinvar id is 1248446.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.892 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASTN2	NM_001365068.1 linkuse as main transcript	c.1482G>A	p.Pro494Pro	synonymous_variant	7/23	ENST00000313400.9	NP_001351997.1
ASTN2	NM_001365069.1 linkuse as main transcript	c.1482G>A	p.Pro494Pro	synonymous_variant	7/23		NP_001351998.1
ASTN2	NM_014010.5 linkuse as main transcript	c.1329G>A	p.Pro443Pro	synonymous_variant	6/22		NP_054729.3	O75129-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ASTN2	ENST00000313400.9 linkuse as main transcript	c.1482G>A	p.Pro494Pro	synonymous_variant	7/23	5	NM_001365068.1	ENSP00000314038.4	O75129-1
ASTN2	ENST00000361209.6 linkuse as main transcript	c.1329G>A	p.Pro443Pro	synonymous_variant	6/22	1		ENSP00000354504.2	O75129-2
ASTN2	ENST00000361477.8 linkuse as main transcript	c.1329G>A	p.Pro443Pro	synonymous_variant	6/23	5		ENSP00000355116.5	A0A0A0MRH9
ASTN2	ENST00000373986.7 linkuse as main transcript	c.663G>A	p.Pro221Pro	synonymous_variant	5/21	2		ENSP00000363098.3	H0Y3A8

Frequencies

GnomAD3 genomes

AF:

0.470

AC:

71395

AN:

151880

Hom.:

19424

Cov.:

show subpopulations

Gnomad AFR

AF:

0.184

Gnomad AMI

AF:

0.652

Gnomad AMR

AF:

0.622

Gnomad ASJ

AF:

0.486

Gnomad EAS

AF:

0.745

Gnomad SAS

AF:

0.505

Gnomad FIN

AF:

0.549

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.570

Gnomad OTH

AF:

0.515

GnomAD3 exomes

AF:

0.559

AC:

138218

AN:

247390

Hom.:

40931

AF XY:

0.555

AC XY:

74279

AN XY:

133724

show subpopulations

Gnomad AFR exome

AF:

0.174

Gnomad AMR exome

AF:

0.712

Gnomad ASJ exome

AF:

0.495

Gnomad EAS exome

AF:

0.747

Gnomad SAS exome

AF:

0.486

Gnomad FIN exome

AF:

0.563

Gnomad NFE exome

AF:

0.563

Gnomad OTH exome

AF:

0.553

GnomAD4 exome

AF:

0.563

AC:

820377

AN:

1457012

Hom.:

235946

Cov.:

AF XY:

0.560

AC XY:

406116

AN XY:

724672

show subpopulations

Gnomad4 AFR exome

AF:

0.163

Gnomad4 AMR exome

AF:

0.704

Gnomad4 ASJ exome

AF:

0.497

Gnomad4 EAS exome

AF:

0.759

Gnomad4 SAS exome

AF:

0.495

Gnomad4 FIN exome

AF:

0.562

Gnomad4 NFE exome

AF:

0.571

Gnomad4 OTH exome

AF:

0.548

GnomAD4 genome

AF:

0.470

AC:

71416

AN:

151998

Hom.:

19425

Cov.:

AF XY:

0.474

AC XY:

35256

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.184

Gnomad4 AMR

AF:

0.621

Gnomad4 ASJ

AF:

0.486

Gnomad4 EAS

AF:

0.744

Gnomad4 SAS

AF:

0.505

Gnomad4 FIN

AF:

0.549

Gnomad4 NFE

AF:

0.570

Gnomad4 OTH

AF:

0.516

Alfa

AF:

0.534

Hom.:

29347

Bravo

AF:

0.468

Asia WGS

AF:

0.572

AC:

1989

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 03, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

3.1

DANN

Benign

0.76

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over