NM_001375380.1(EBF3):c.486-1G>A AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 11, 2017
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000495980.1

Allele description [Variation Report for NM_001375380.1(EBF3):c.486-1G>A]

NM_001375380.1(EBF3):c.486-1G>A

Gene:

EBF3:EBF transcription factor 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q26.3

Genomic location:

Preferred name:

NM_001375380.1(EBF3):c.486-1G>A

HGVS:

NC_000010.11:g.129957327C>T
NG_030038.1:g.11501G>A
NM_001005463.3:c.486-1G>A
NM_001375379.1:c.486-1G>A
NM_001375380.1:c.486-1G>AMANE SELECT
NM_001375389.1:c.486-1G>A
NM_001375390.1:c.486-1G>A
NM_001375391.1:c.486-1G>A
NM_001375392.1:c.486-1G>A
NC_000010.10:g.131755591C>T
NM_001005463.2:c.486-1G>A

Links:

dbSNP: rs1131692258

NCBI 1000 Genomes Browser:

rs1131692258

Molecular consequence:

NM_001005463.3:c.486-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001375379.1:c.486-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001375380.1:c.486-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001375389.1:c.486-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001375390.1:c.486-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001375391.1:c.486-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001375392.1:c.486-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000584020	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Jul 11, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000584020

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Jul 11, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000584020.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The c.486-1G>A variant in the EBF3 gene has been observed in internal GeneDx whole exome sequencing data in association with intellectual disability, autistic features, hypotonia, short stature, vermis hypoplasia, and facial dysmorphism. This splice site variant destroys the canonical splice acceptor site in intron 5, which is predicted to cause abnormal gene splicing. The c.486-1G>A variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret c.486-1G>A as a pathogenic variant.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 16, 2024

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