NM_000141.5(FGFR2):c.940-2A>G AND Pfeiffer syndrome

Germline classification:: Conflicting classifications of pathogenicity (3 submissions)
Last evaluated:: Mar 26, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV000415479.8

Allele description [Variation Report for NM_000141.5(FGFR2):c.940-2A>G]

NM_000141.5(FGFR2):c.940-2A>G

Gene:

FGFR2:fibroblast growth factor receptor 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q26.13

Genomic location:

Preferred name:

NM_000141.5(FGFR2):c.940-2A>G

HGVS:

NC_000010.11:g.121517465T>C
NG_012449.2:g.85994A>G
NM_000141.5:c.940-2A>GMANE SELECT
NM_001144913.1:c.1087+1217A>G
NM_001144914.1:c.749-2146A>G
NM_001144915.2:c.673-2A>G
NM_001144916.2:c.595-2A>G
NM_001144917.2:c.939+2514A>G
NM_001144918.2:c.595-2A>G
NM_001144919.2:c.820+1217A>G
NM_001320654.2:c.256-2A>G
NM_001320658.2:c.940-2A>G
NM_022970.4:c.1087+1217A>G
NM_023029.2:c.673-2A>G
LRG_994t1:c.940-2A>G
LRG_994:g.85994A>G
NC_000010.10:g.123276979T>C
NM_000141.4:c.940-2A>G

Links:

dbSNP: rs1057519041

NCBI 1000 Genomes Browser:

rs1057519041

Molecular consequence:

NM_001144913.1:c.1087+1217A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001144914.1:c.749-2146A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001144917.2:c.939+2514A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001144919.2:c.820+1217A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_022970.4:c.1087+1217A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000141.5:c.940-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001144915.2:c.673-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001144916.2:c.595-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001144918.2:c.595-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001320654.2:c.256-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001320658.2:c.940-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_023029.2:c.673-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]

Observations:

Condition(s)

Name:: Pfeiffer syndrome (ACS5)
Synonyms:: ACS V
Identifiers:: MONDO: MONDO:0007043; MedGen: C0220658; Orphanet: 710; OMIM: 101600

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000328382	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	criteria provided, single submitter (DGD Variant Analysis Guidelines)	Pathogenic (Sep 17, 2016)	germline	clinical testing	Citation Link,
SCV000996314	Clinical Genetics Laboratory, Federal University of Health Sciences of Porto Alegre	no assertion criteria provided	Pathogenic (Mar 14, 2014)	de novo	research
SCV004807327	Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Mar 26, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000328382

Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia

criteria provided, single submitter

(DGD Variant Analysis Guidelines)

Pathogenic
(Sep 17, 2016)

germline

clinical testing

Citation Link,

SCV000996314

Clinical Genetics Laboratory, Federal University of Health Sciences of Porto Alegre

no assertion criteria provided

Pathogenic
(Mar 14, 2014)

de novo

research

SCV004807327

Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Mar 26, 2024)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	de novo	yes	1	not provided	not provided	1	not provided	research

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 Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, SCV000328382.2

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

From Clinical Genetics Laboratory, Federal University of Health Sciences of Porto Alegre, SCV000996314.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	de novo	yes	1	not provided	discovery		1	not provided	not provided	not provided

From Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre, SCV004807327.1

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 14, 2025

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