NM_006892.4(DNMT3B):c.2421-11G>A AND not provided

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Dec 14, 2022
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:: RCV001268751.3

Allele description [Variation Report for NM_006892.4(DNMT3B):c.2421-11G>A]

NM_006892.4(DNMT3B):c.2421-11G>A

Gene:

DNMT3B:DNA methyltransferase 3 beta [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

20q11.21

Genomic location:

Preferred name:

NM_006892.4(DNMT3B):c.2421-11G>A

HGVS:

NC_000020.11:g.32807751G>A
NG_007290.1:g.50367G>A
NM_001207055.2:c.2046-11G>A
NM_001207056.2:c.1944-11G>A
NM_006892.4:c.2421-11G>AMANE SELECT
NM_175848.2:c.2361-11G>A
NM_175849.2:c.2172-11G>A
NM_175850.3:c.2397-11G>A
LRG_56:g.50367G>A
NC_000020.10:g.31395557G>A
NM_175850.2:c.2397-11G>A

Note:

NCBI staff reviewed the sequence information reported in PubMed 10555141 Fig. 8D to determine the location of this allele on the current reference sequence.

Nucleotide change:

IVS22AS, G-A, -11

Links:

OMIM: 602900.0009; dbSNP: rs547940069

NCBI 1000 Genomes Browser:

rs547940069

Molecular consequence:

NM_001207055.2:c.2046-11G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001207056.2:c.1944-11G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_006892.4:c.2421-11G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_175848.2:c.2361-11G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_175849.2:c.2172-11G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_175850.3:c.2397-11G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Tadorna tadorna Sox2 (Sox2) cds
Tadorna tadorna Sox2 (Sox2) cds
gi|161075468|gb|EU244486.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001447909	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 23, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003933495	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Dec 14, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001447909

Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Oct 23, 2020)

germline

clinical testing

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

SCV003933495

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Dec 14, 2022)

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	1	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 Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, SCV001447909.1

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

From GeneDx, SCV003933495.1

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

Description

Reported with another DNMT3B variant in at least two unrelated individuals with ICF syndrome, but it is not known whether the variants occurred on the same (in cis) or on different (in trans) chromosomes (Okano et al.,1999, Hansen et al., 1999; Jiang et al., 2005); Published functional studies suggest this variant results in aberrant splicing (Okano et al., 1999); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 31589614, 28334849, 22378288, 10555141, 27153398, 17893117, 28916186, 21147113, 9718351, 3361388, Shirkani_2020, 23486536, 17908720, 15580563, 10588719, 11102980)

#	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: Sep 29, 2024

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