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

Germline classification:: Pathogenic (1 submission)
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV004796173.1

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]

Condition(s)

Name:: Acrocephalosyndactyly type I (ACS1)
Synonyms:: Apert syndrome; Acrocephalo-syndactyly type 1; ACS 1; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007041; MedGen: C0001193; Orphanet: 87; OMIM: 101200

Name:: Beare-Stevenson cutis gyrata syndrome (BSTVS)
Identifiers:: MONDO: MONDO:0007412; MedGen: C1852406; Orphanet: 1555; OMIM: 123790

Name:: Jackson-Weiss syndrome (JWS)
Synonyms:: CRANIOSYNOSTOSIS, MIDFACIAL HYPOPLASIA, AND FOOT ABNORMALITIES
Identifiers:: MONDO: MONDO:0007400; MedGen: C0795998; Orphanet: 1540; OMIM: 123150

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

Name:: Antley-Bixler syndrome without genital anomalies or disordered steroidogenesis (ABS2)
Synonyms:: MULTISYNOSTOTIC OSTEODYSGENESIS WITH LONG BONE FRACTURES; Antley-Bixler Syndrome, Autosomal Dominant; Trapezoidocephaly synostosis syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0020667; MedGen: C2936791; Orphanet: 83; OMIM: 207410

Name:: Crouzon syndrome
Synonyms:: CRANIOFACIAL DYSOSTOSIS, TYPE I; Crouzon craniofacial dysostosis; Crouzon disease; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007405; MeSH: D003394; MedGen: C0010273; Orphanet: 207; OMIM: 123500; Human Phenotype Ontology: HP:0004439

Name:: Saethre-Chotzen syndrome (SCS)
Synonyms:: ACROCEPHALY, SKULL ASYMMETRY, AND MILD SYNDACTYLY; ACS III; CHOTZEN SYNDROME
Identifiers:: MONDO: MONDO:0007042; MedGen: C0175699; Orphanet: 794; OMIM: 101400

Name:: Familial scaphocephaly syndrome, McGillivray type
Synonyms:: SCAPHOCEPHALY, MAXILLARY RETRUSION, AND IMPAIRED INTELLECTUAL DEVELOPMENT
Identifiers:: MONDO: MONDO:0012307; MedGen: C1865070; Orphanet: 168624; OMIM: 609579

Name:: Bent bone dysplasia syndrome 1 (BBDS1)
Synonyms:: FGFR2-related bent bone dysplasia
Identifiers:: MONDO: MONDO:0013815; MedGen: C3281247; Orphanet: 313855; OMIM: 614592

Name:: Gastric cancer
Synonyms:: Stomach cancer; Malignant tumor of stomach
Identifiers:: MONDO: MONDO:0001056; MeSH: D013274; MedGen: C0024623; OMIM: 613659; Human Phenotype Ontology: HP:0012126

Name:: LADD syndrome 1 (LADD1)
Synonyms:: Lacrimoauriculodentodigital syndrome 1
Identifiers:: MONDO: MONDO:0100302; MedGen: C5774323; OMIM: 149730

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005418479	Juno Genomics, Hangzhou Juno Genomics, Inc	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	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

SCV005418479

Juno Genomics, Hangzhou Juno Genomics, Inc

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic

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	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 Juno Genomics, Hangzhou Juno Genomics, Inc, SCV005418479.1

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

Description

PVS1+PM2_Supporting+PS4+PM6

#	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: Jun 14, 2025

ClinVar

Relating variation to medicine