U.S. flag

An official website of the United States government

NM_023110.3(FGFR1):c.-209G>C AND Hypogonadotropic hypogonadism 2 with or without anosmia

Germline classification:
Likely benign (1 submission)
Last evaluated:
Jan 12, 2018
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:
RCV001158711.4

Allele description [Variation Report for NM_023110.3(FGFR1):c.-209G>C]

NM_023110.3(FGFR1):c.-209G>C

Genes:
LOC130000233:ATAC-STARR-seq lymphoblastoid silent region 19129 [Gene]
FGFR1:fibroblast growth factor receptor 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
8p11.23
Genomic location:
Preferred name:
NM_023110.3(FGFR1):c.-209G>C
HGVS:
  • NC_000008.11:g.38468101C>G
  • NG_007729.1:g.5734G>C
  • NM_001174063.2:c.-209G>C
  • NM_001174064.2:c.-301G>C
  • NM_001354367.2:c.-209G>C
  • NM_001354368.2:c.-209G>C
  • NM_001354370.2:c.-209G>C
  • NM_015850.4:c.-209G>C
  • NM_023105.3:c.-209G>C
  • NM_023106.3:c.-209G>C
  • NM_023110.3:c.-209G>CMANE SELECT
  • LRG_993t1:c.-209G>C
  • LRG_993:g.5734G>C
  • NC_000008.10:g.38325619C>G
  • NM_023110.2:c.-209G>C
Links:
dbSNP: rs572216432
NCBI 1000 Genomes Browser:
rs572216432
Molecular consequence:
  • NM_001174063.2:c.-209G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001174064.2:c.-301G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354367.2:c.-209G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354368.2:c.-209G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354370.2:c.-209G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_015850.4:c.-209G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_023105.3:c.-209G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_023106.3:c.-209G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_023110.3:c.-209G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

Condition(s)

Name:
Hypogonadotropic hypogonadism 2 with or without anosmia (HH2)
Synonyms:
Kallmann syndrome 2; HYPOGONADOTROPIC HYPOGONADISM 2 WITHOUT ANOSMIA; HYPOGONADOTROPIC HYPOGONADISM 2 WITH OR WITHOUT ANOSMIA, SUSCEPTIBILITY TO; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0007844; MedGen: C1563720; Orphanet: 478; OMIM: 147950

Recent activity

Clear Turn Off Turn On
  • Plant sample from Cornus sanguinea
    Plant sample from Cornus sanguinea
    biosample
  • Limbic Lobe
    Limbic Lobe
    The medial surface of the cerebral hemisphere around the brain stem.<br/>Year introduced: 2015
    MeSH
  • Substantia Innominata
    Substantia Innominata
    Tissue in the BASAL FOREBRAIN inferior to the anterior perforated substance, and anterior to the GLOBUS PALLIDUS and ansa lenticularis. It contains the BASAL NUCLEUS OF MEYNER...<br/>Year introduced: 1991(1984)
    MeSH
  • Hypothalamus
    Hypothalamus
    Ventral part of the DIENCEPHALON extending from the region of the OPTIC CHIASM to the caudal border of the MAMMILLARY BODIES and forming the inferior and lateral walls of the ...<br/>
    MeSH
  • Glymphatic System
    Glymphatic System
    A vascular waste clearance system in the brain analogous to the lymphatic system that facilitates transporting of solutes and waste products from CEREBROSPINAL FLUID (CSF) and...<br/>Year introduced: 2019
    MeSH

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001320364Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)		Likely benign
(Jan 12, 2018) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001320364.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Dec 24, 2023