NM_001354604.2(MITF):c.1566G>A (p.Thr522=) AND not specified

Germline classification:: Benign (3 submissions)
Last evaluated:: Feb 6, 2018
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:: RCV000220011.7

Allele description [Variation Report for NM_001354604.2(MITF):c.1566G>A (p.Thr522=)]

NM_001354604.2(MITF):c.1566G>A (p.Thr522=)

Gene:

MITF:melanocyte inducing transcription factor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p13

Genomic location:

Preferred name:

NM_001354604.2(MITF):c.1566G>A (p.Thr522=)

HGVS:

NC_000003.12:g.69965233G>A
NG_011631.1:g.230752G>A
NM_000248.4:c.1245G>A
NM_001184967.2:c.1392G>A
NM_001354604.2:c.1566G>AMANE SELECT
NM_001354605.2:c.1563G>A
NM_001354606.2:c.1545G>A
NM_001354607.2:c.1497G>A
NM_001354608.2:c.1392G>A
NM_006722.3:c.1545G>A
NM_198158.3:c.1227G>A
NM_198159.3:c.1548G>A
NM_198177.3:c.1500G>A
NM_198178.3:c.1059G>A
NP_000239.1:p.Thr415=
NP_000239.1:p.Thr415=
NP_001171896.1:p.Thr464=
NP_001341533.1:p.Thr522=
NP_001341534.1:p.Thr521=
NP_001341535.1:p.Thr515=
NP_001341536.1:p.Thr499=
NP_001341537.1:p.Thr464=
NP_006713.1:p.Thr515=
NP_937801.1:p.Thr409=
NP_937802.1:p.Thr516=
NP_937820.1:p.Thr500=
NP_937821.2:p.Thr353=
LRG_776t1:c.1245G>A
LRG_776:g.230752G>A
LRG_776p1:p.Thr415=
NC_000003.11:g.70014384G>A
NM_000248.3:c.1245G>A
NM_198159.2:c.1548G>A
p.Thr516Thr

Links:

dbSNP: rs36118030

NCBI 1000 Genomes Browser:

rs36118030

Molecular consequence:

NM_000248.4:c.1245G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001184967.2:c.1392G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354604.2:c.1566G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354605.2:c.1563G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354606.2:c.1545G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354607.2:c.1497G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354608.2:c.1392G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_006722.3:c.1545G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_198158.3:c.1227G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_198159.3:c.1548G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_198177.3:c.1500G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_198178.3:c.1059G>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
SCV000269240	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Nov 24, 2014)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000713874	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Feb 6, 2018)	germline	clinical testing	Citation Link,
SCV003839717	Genetic Services Laboratory, University of Chicago	no assertion criteria provided	Benign (May 12, 2022)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000269240

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Benign
(Nov 24, 2014)

germline

clinical testing

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

SCV000713874

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Benign
(Feb 6, 2018)

germline

clinical testing

Citation Link,

SCV003839717

Genetic Services Laboratory, University of Chicago

no assertion criteria provided

Benign
(May 12, 2022)

germline

clinical testing

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
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	11	11	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, SCV000269240.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	11	not provided	not provided	clinical testing	PubMed (1)

Description

Thr516Thr in exon 10 of MITF: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue and is not located with in the splice consensus sequence. It has been identified in 2.7% (120/4406) of A frican American chromosomes from a broad population by the NHLBI Exome Sequencin g Project (http://evs.gs.washington.edu/EVS; dbSNP rs36118030).

#	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		11	not provided	11	not provided

From GeneDx, SCV000713874.1

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	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

From Genetic Services Laboratory, University of Chicago, SCV003839717.1

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 24, 2023

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