NM_020717.5(SHROOM4):c.3414A>G (p.Glu1138=) AND not specified

Germline classification:: Benign (3 submissions)
Last evaluated:: Sep 25, 2015
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:: RCV000082026.21

Allele description [Variation Report for NM_020717.5(SHROOM4):c.3414A>G (p.Glu1138=)]

NM_020717.5(SHROOM4):c.3414A>G (p.Glu1138=)

Gene:

SHROOM4:shroom family member 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp11.22

Genomic location:

Preferred name:

NM_020717.5(SHROOM4):c.3414A>G (p.Glu1138=)

HGVS:

NC_000023.11:g.50607728T>C
NG_011882.1:g.211317A>G
NM_020717.5:c.3414A>GMANE SELECT
NP_065768.2:p.Glu1138=
NP_065768.2:p.Glu1138=
NC_000023.10:g.50350728T>C
NM_020717.3:c.3414A>G
NP_065768.2:p.(=)
NR_027121.3:n.3590A>G
NR_172068.1:n.3455A>G
NR_172069.1:n.3510A>G
NR_172070.1:n.3375A>G

Links:

dbSNP: rs6614552

NCBI 1000 Genomes Browser:

rs6614552

Molecular consequence:

NR_027121.3:n.3590A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_172068.1:n.3455A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_172069.1:n.3510A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_172070.1:n.3375A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_020717.5:c.3414A>G - 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
SCV000113961	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Benign (Sep 25, 2015)	germline	clinical testing	Citation Link,
SCV000152745	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2007)	Benign (Oct 11, 2013)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000851816	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Benign (Jul 12, 2015)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000113961

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Benign
(Sep 25, 2015)

germline

clinical testing

Citation Link,

SCV000152745

Genetic Services Laboratory, University of Chicago

criteria provided, single submitter

(ACMG Guidelines, 2007)

Benign
(Oct 11, 2013)

germline

clinical testing

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

SCV000851816

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Benign
(Jul 12, 2015)

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	unknown	5	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.

Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee..

Genet Med. 2008 Apr;10(4):294-300. doi: 10.1097/GIM.0b013e31816b5cae.

PubMed [citation]

PMID:: 18414213

Details of each submission

From Eurofins Ntd Llc (ga), SCV000113961.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	5	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		5	not provided	not provided	not provided

From Genetic Services Laboratory, University of Chicago, SCV000152745.1

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

#	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

From Ambry Genetics, SCV000851816.5

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

Description

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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: Oct 13, 2024

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