Variant rs2293508 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_015570.4(AUTS2):c.1026A>G(p.Pro342=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0525 in 1,613,838 control chromosomes in the GnomAD database, including 3,555 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.092 ( 1085 hom., cov: 32)

Exomes 𝑓: 0.048 ( 2470 hom. )

Consequence

AUTS2
NM_015570.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.27

Variant links:

Genes affected

AUTS2 (HGNC:14262): (activator of transcription and developmental regulator AUTS2) This gene has been implicated in neurodevelopment and as a candidate gene for numerous neurological disorders, including autism spectrum disorders, intellectual disability, and developmental delay. Mutations in this gene have also been associated with non-neurological disorders, such as acute lymphoblastic leukemia, aging of the skin, early-onset androgenetic alopecia, and certain cancers. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2014]

AUTS2 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=-0.96).

BP6

Variant 7-70763153-A-G is Benign according to our data. Variant chr7-70763153-A-G is described in ClinVar as [Benign]. Clinvar id is 1227066.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.27 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AUTS2	NM_015570.4 linkuse as main transcript	c.1026A>G	p.Pro342=	synonymous_variant	7/19	ENST00000342771.10	NP_056385.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AUTS2	ENST00000342771.10 linkuse as main transcript	c.1026A>G	p.Pro342=	synonymous_variant	7/19	1	NM_015570.4	ENSP00000344087	P4	Q8WXX7-1

Frequencies

GnomAD3 genomes

AF:

0.0917

AC:

13938

AN:

151980

Hom.:

1078

Cov.:

show subpopulations

Gnomad AFR

AF:

0.212

Gnomad AMI

AF:

0.0932

Gnomad AMR

AF:

0.0633

Gnomad ASJ

AF:

0.110

Gnomad EAS

AF:

0.0760

Gnomad SAS

AF:

0.0776

Gnomad FIN

AF:

0.00519

Gnomad MID

AF:

0.156

Gnomad NFE

AF:

0.0389

Gnomad OTH

AF:

0.100

GnomAD3 exomes

AF:

0.0594

AC:

14862

AN:

250036

Hom.:

763

AF XY:

0.0580

AC XY:

7843

AN XY:

135266

show subpopulations

Gnomad AFR exome

AF:

0.212

Gnomad AMR exome

AF:

0.0414

Gnomad ASJ exome

AF:

0.102

Gnomad EAS exome

AF:

0.0747

Gnomad SAS exome

AF:

0.0797

Gnomad FIN exome

AF:

0.00634

Gnomad NFE exome

AF:

0.0412

Gnomad OTH exome

AF:

0.0663

GnomAD4 exome

AF:

0.0484

AC:

70727

AN:

1461740

Hom.:

2470

Cov.:

AF XY:

0.0488

AC XY:

35506

AN XY:

727156

show subpopulations

Gnomad4 AFR exome

AF:

0.211

Gnomad4 AMR exome

AF:

0.0442

Gnomad4 ASJ exome

AF:

0.103

Gnomad4 EAS exome

AF:

0.0605

Gnomad4 SAS exome

AF:

0.0803

Gnomad4 FIN exome

AF:

0.00701

Gnomad4 NFE exome

AF:

0.0403

Gnomad4 OTH exome

AF:

0.0636

GnomAD4 genome

AF:

0.0918

AC:

13963

AN:

152098

Hom.:

1085

Cov.:

AF XY:

0.0886

AC XY:

6586

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.212

Gnomad4 AMR

AF:

0.0632

Gnomad4 ASJ

AF:

0.110

Gnomad4 EAS

AF:

0.0761

Gnomad4 SAS

AF:

0.0774

Gnomad4 FIN

AF:

0.00519

Gnomad4 NFE

AF:

0.0389

Gnomad4 OTH

AF:

0.0999

Alfa

AF:

0.0666

Hom.:

265

Bravo

AF:

0.101

Asia WGS

AF:

0.0970

AC:

337

AN:

3478

EpiCase

AF:

0.0507

EpiControl

AF:

0.0489

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 15, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.029

DANN

Benign

0.28

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

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