NM_153759.3(DNMT3A):c.1937C>T (p.Thr646Met) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Mar 22, 2023
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:: RCV002221939.3

Allele description [Variation Report for NM_153759.3(DNMT3A):c.1937C>T (p.Thr646Met)]

NM_153759.3(DNMT3A):c.1937C>T (p.Thr646Met)

Gene:

DNMT3A:DNA methyltransferase 3 alpha [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Preferred name:

NM_153759.3(DNMT3A):c.1937C>T (p.Thr646Met)

HGVS:

NC_000002.12:g.25235800G>A
NG_029465.2:g.111791C>T
NM_001320893.1:c.2048C>T
NM_001375819.1:c.1835C>T
NM_022552.5:c.2504C>TMANE SELECT
NM_153759.3:c.1937C>T
NM_175629.2:c.2504C>T
NP_001307822.1:p.Thr683Met
NP_001362748.1:p.Thr612Met
NP_072046.2:p.Thr835Met
NP_715640.2:p.Thr646Met
NP_783328.1:p.Thr835Met
LRG_459t2:c.1937C>T
LRG_459t4:c.2504C>T
LRG_459:g.111791C>T
LRG_459p2:p.Thr646Met
LRG_459p4:p.Thr835Met
NC_000002.11:g.25458669G>A
NR_135490.2:n.2934C>T

Protein change:

T612M

Links:

dbSNP: rs1489843853

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
SCV002499224	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jan 25, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004036261	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Mar 22, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002499224

Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jan 25, 2022)

germline

clinical testing

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

SCV004036261

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Mar 22, 2023)

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center, SCV002499224.1

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

Description

PM2, PP3, PP2

#	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 GeneDx, SCV004036261.1

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

#	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: Dec 24, 2023

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