chr11-69774864-C-T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_002007.4(FGF4):c.221G>A(p.Gly74Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 34)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
FGF4
NM_002007.4 missense
NM_002007.4 missense
Scores
3
8
7
Clinical Significance
Conservation
PhyloP100: 3.55
Publications
0 publications found
Genes affected
FGF4 (HGNC:3682): (fibroblast growth factor 4) The protein encoded by this gene is a member of the fibroblast growth factor (FGF) family. FGF family members possess broad mitogenic and cell survival activities and are involved in a variety of biological processes including embryonic development, cell growth, morphogenesis, tissue repair, tumor growth and invasion. This gene was identified by its oncogenic transforming activity. This gene and FGF3, another oncogenic growth factor, are located closely on chromosome 11. Co-amplification of both genes was found in various kinds of human tumors. Studies on the mouse homolog suggested a function in bone morphogenesis and limb development through the sonic hedgehog (SHH) signaling pathway. [provided by RefSeq, Jul 2008]
FGF4 Gene-Disease associations (from GenCC):
- thoracic malformationInheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_002007.4. You can select a different transcript below to see updated ACMG assignments.
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
34
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1355524Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 669702
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1355524
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
669702
African (AFR)
AF:
AC:
0
AN:
27846
American (AMR)
AF:
AC:
0
AN:
32854
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
23978
East Asian (EAS)
AF:
AC:
0
AN:
30930
South Asian (SAS)
AF:
AC:
0
AN:
76496
European-Finnish (FIN)
AF:
AC:
0
AN:
34006
Middle Eastern (MID)
AF:
AC:
0
AN:
4794
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1068058
Other (OTH)
AF:
AC:
0
AN:
56562
GnomAD4 genome
GnomAD4 genome
Cov.:
34
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Uncertain
D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
M_CAP
Pathogenic
D
MetaRNN
Uncertain
D
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
M
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Benign
N
REVEL
Uncertain
Sift
Benign
T
Sift4G
Benign
T
Polyphen
P
Vest4
MutPred
Loss of MoRF binding (P = 0.0638)
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
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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