chr7-69899331-A-ACGCCC

Variant names:

• chr7-69899331-A-ACGCCC
• rs1554401434
• NM_015570.4:c.357_361dupGCCCC

Variant summary

Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PVS1 PM2 PP5

The NM_015570.4(AUTS2):​c.357_361dupGCCCC​(p.Leu121ArgfsTer3) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: AUTS2 NM_015570.4 frameshift
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 1.57
• Publications: 0 publications found

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 Gene-Disease associations (from GenCC):

• autism spectrum disorder due to AUTS2 deficiency

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Orphanet
• syndromic intellectual disability

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen

ACMG classification

Our verdict: Pathogenic. The variant received 11 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 7-69899331-A-ACGCCC is Pathogenic according to our data. Variant chr7-69899331-A-ACGCCC is described in ClinVar as Pathogenic. ClinVar VariationId is 559629.Status of the report is no_assertion_criteria_provided, 0 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015570.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AUTS2	NM_015570.4	MANE Select	c.357_361dupGCCCC	p.Leu121ArgfsTer3	frameshift	Exon 2 of 19	NP_056385.1
	AUTS2	NM_001127231.3		c.357_361dupGCCCC	p.Leu121ArgfsTer3	frameshift	Exon 2 of 18	NP_001120703.1
	AUTS2	NM_001127232.3		c.357_361dupGCCCC	p.Leu121ArgfsTer3	frameshift	Exon 2 of 5	NP_001120704.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AUTS2	ENST00000342771.10	TSL:1 MANE Select	c.357_361dupGCCCC	p.Leu121ArgfsTer3	frameshift	Exon 2 of 19	ENSP00000344087.4
	AUTS2	ENST00000406775.6	TSL:1	c.357_361dupGCCCC	p.Leu121ArgfsTer3	frameshift	Exon 2 of 18	ENSP00000385263.2
	AUTS2	ENST00000403018.3	TSL:1	c.357_361dupGCCCC	p.Leu121ArgfsTer3	frameshift	Exon 2 of 5	ENSP00000385572.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Autism spectrum disorder due to AUTS2 deficiency Pathogenic:1

Dec 14, 2017

Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.6
Mutation Taster		=0/200	disease causing (ClinVar)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1554401434; hg19: chr7-69364317;