NM_004100.5(EYA4):c.783G>A (p.Thr261=) AND not specified

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Jan 28, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000037881.7

Allele description [Variation Report for NM_004100.5(EYA4):c.783G>A (p.Thr261=)]

NM_004100.5(EYA4):c.783G>A (p.Thr261=)

Gene:

EYA4:EYA transcriptional coactivator and phosphatase 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q23.2

Genomic location:

Preferred name:

NM_004100.5(EYA4):c.783G>A (p.Thr261=)

HGVS:

NC_000006.12:g.133464837G>A
NG_011596.2:g.228481G>A
NM_001301012.2:c.621G>A
NM_001301013.2:c.783G>A
NM_001370458.1:c.714G>A
NM_001370459.1:c.621G>A
NM_004100.5:c.783G>AMANE SELECT
NM_172103.4:c.714G>A
NM_172105.4:c.783G>A
NP_001287941.1:p.Thr207=
NP_001287942.1:p.Thr261=
NP_001357387.1:p.Thr238=
NP_001357388.1:p.Thr207=
NP_004091.3:p.Thr261=
NP_742101.2:p.Thr238=
NP_742103.1:p.Thr261=
NP_742103.1:p.Thr261=
LRG_418t1:c.783G>A
LRG_418:g.228481G>A
LRG_418p1:p.Thr261=
NC_000006.11:g.133785975G>A
NM_004100.4:c.783G>A
NM_172105.3:c.783G>A
c.783G>A
p.Thr261Thr

Links:

dbSNP: rs17854076

NCBI 1000 Genomes Browser:

rs17854076

Molecular consequence:

NM_001301012.2:c.621G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001301013.2:c.783G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001370458.1:c.714G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001370459.1:c.621G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_004100.5:c.783G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_172103.4:c.714G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_172105.4:c.783G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000061543	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Likely benign (Oct 3, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001478746	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Jan 28, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000061543

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Likely benign
(Oct 3, 2017)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001478746

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Benign
(Jan 28, 2021)

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	not provided	3	3	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000061543.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	not provided	not provided	clinical testing	PubMed (1)

Description

p.Thr261Thr in exon 10 of EYA4: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, is not located withi n the splice consensus sequence, and has been identified in 0.24% (306/126180) o f European chromosomes including 1 homozygote by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs17854076).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		3	not provided	3	not provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001478746.1

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

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

Last Updated: Sep 29, 2024

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