rs2912771
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000141.5(FGFR2):c.625-1068C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 152,132 control chromosomes in the GnomAD database, including 31,613 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.62 ( 31613 hom., cov: 34)
Consequence
FGFR2
NM_000141.5 intron
NM_000141.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.144
Publications
4 publications found
Genes affected
FGFR2 (HGNC:3689): (fibroblast growth factor receptor 2) The protein encoded by this gene is a member of the fibroblast growth factor receptor family, where amino acid sequence is highly conserved between members and throughout evolution. FGFR family members differ from one another in their ligand affinities and tissue distribution. A full-length representative protein consists of an extracellular region, composed of three immunoglobulin-like domains, a single hydrophobic membrane-spanning segment and a cytoplasmic tyrosine kinase domain. The extracellular portion of the protein interacts with fibroblast growth factors, setting in motion a cascade of downstream signals, ultimately influencing mitogenesis and differentiation. This particular family member is a high-affinity receptor for acidic, basic and/or keratinocyte growth factor, depending on the isoform. Mutations in this gene are associated with Crouzon syndrome, Pfeiffer syndrome, Craniosynostosis, Apert syndrome, Jackson-Weiss syndrome, Beare-Stevenson cutis gyrata syndrome, Saethre-Chotzen syndrome, and syndromic craniosynostosis. Multiple alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Jan 2009]
FGFR2 Gene-Disease associations (from GenCC):
- Apert syndromeInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, ClinGen, PanelApp Australia, G2P, Genomics England PanelApp
- Beare-Stevenson cutis gyrata syndromeInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, ClinGen, G2P, Genomics England PanelApp
- Crouzon syndromeInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, ClinGen, PanelApp Australia, Genomics England PanelApp, G2P
- Jackson-Weiss syndromeInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Genomics England PanelApp, G2P
- LADD syndrome 1Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
- Pfeiffer syndromeInheritance: AD Classification: DEFINITIVE, STRONG Submitted by: ClinGen, PanelApp Australia, Labcorp Genetics (formerly Invitae), Ambry Genetics, Genomics England PanelApp, G2P
- Antley-Bixler syndrome without genital anomalies or disordered steroidogenesisInheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp, G2P
- bent bone dysplasia syndrome 1Inheritance: AD Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Orphanet
- familial scaphocephaly syndrome, McGillivray typeInheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Genomics England PanelApp
- Saethre-Chotzen syndromeInheritance: AD Classification: STRONG Submitted by: PanelApp Australia, Genomics England PanelApp
- Antley-Bixler syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- LADD syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Pfeiffer syndrome type 1Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Pfeiffer syndrome type 2Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Pfeiffer syndrome type 3Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FGFR2 | ENST00000358487.10 | c.625-1068C>T | intron_variant | Intron 5 of 17 | 1 | NM_000141.5 | ENSP00000351276.6 | |||
FGFR2 | ENST00000457416.7 | c.625-1068C>T | intron_variant | Intron 5 of 17 | 1 | ENSP00000410294.2 | ||||
FGFR2 | ENST00000369056.5 | c.625-1068C>T | intron_variant | Intron 4 of 16 | 1 | ENSP00000358052.1 | ||||
FGFR2 | ENST00000369058.7 | c.625-1068C>T | intron_variant | Intron 5 of 16 | 1 | ENSP00000358054.3 | ||||
FGFR2 | ENST00000613048.4 | c.358-1068C>T | intron_variant | Intron 4 of 16 | 5 | ENSP00000484154.1 | ||||
FGFR2 | ENST00000369061.8 | c.625-1068C>T | intron_variant | Intron 4 of 14 | 1 | ENSP00000358057.4 | ||||
FGFR2 | ENST00000369059.5 | c.280-1068C>T | intron_variant | Intron 3 of 15 | 5 | ENSP00000358055.1 | ||||
FGFR2 | ENST00000360144.7 | c.358-1068C>T | intron_variant | Intron 4 of 16 | 2 | ENSP00000353262.3 | ||||
FGFR2 | ENST00000604236.5 | n.280-1068C>T | intron_variant | Intron 3 of 16 | 1 | ENSP00000474109.1 |
Frequencies
GnomAD3 genomes AF: 0.617 AC: 93818AN: 152014Hom.: 31615 Cov.: 34 show subpopulations
GnomAD3 genomes
AF:
AC:
93818
AN:
152014
Hom.:
Cov.:
34
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.617 AC: 93826AN: 152132Hom.: 31613 Cov.: 34 AF XY: 0.617 AC XY: 45850AN XY: 74352 show subpopulations
GnomAD4 genome
AF:
AC:
93826
AN:
152132
Hom.:
Cov.:
34
AF XY:
AC XY:
45850
AN XY:
74352
show subpopulations
African (AFR)
AF:
AC:
13350
AN:
41498
American (AMR)
AF:
AC:
10158
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
2770
AN:
3472
East Asian (EAS)
AF:
AC:
4325
AN:
5168
South Asian (SAS)
AF:
AC:
3460
AN:
4814
European-Finnish (FIN)
AF:
AC:
7103
AN:
10564
Middle Eastern (MID)
AF:
AC:
228
AN:
294
European-Non Finnish (NFE)
AF:
AC:
50372
AN:
68012
Other (OTH)
AF:
AC:
1398
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1658
3316
4973
6631
8289
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
758
1516
2274
3032
3790
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2545
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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