rs1244139413
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000800.5(FGF1):c.344A>T(p.Lys115Met) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,744 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
FGF1
NM_000800.5 missense
NM_000800.5 missense
Scores
10
9
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.79
Genes affected
FGF1 (HGNC:3665): (fibroblast growth factor 1) 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 protein functions as a modifier of endothelial cell migration and proliferation, as well as an angiogenic factor. It acts as a mitogen for a variety of mesoderm- and neuroectoderm-derived cells in vitro, thus is thought to be involved in organogenesis. Multiple alternatively spliced variants encoding different isoforms have been described. [provided by RefSeq, Jan 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| FGF1 | NM_000800.5 | c.344A>T | p.Lys115Met | missense_variant | Exon 4 of 4 | ENST00000337706.7 | NP_000791.1 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461744Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727176
GnomAD4 exome
AF:
AC:
1
AN:
1461744
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
727176
Gnomad4 AFR exome
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Gnomad4 ASJ exome
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Gnomad4 EAS exome
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Gnomad4 SAS exome
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GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
D;D;D;D;D;D;D;D;D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;.;.;D;.;.;.;.;.
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D;D;D;D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;L;L;L;L;L;L;L
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.;.;.;.;N;N;N;N
REVEL
Benign
Sift
Uncertain
D;.;.;.;.;D;D;D;D
Sift4G
Benign
T;T;T;T;T;T;T;T;T
Polyphen
D;D;D;D;D;D;D;D;D
Vest4
MutPred
Loss of catalytic residue at K115 (P = 0.0171);Loss of catalytic residue at K115 (P = 0.0171);Loss of catalytic residue at K115 (P = 0.0171);Loss of catalytic residue at K115 (P = 0.0171);Loss of catalytic residue at K115 (P = 0.0171);Loss of catalytic residue at K115 (P = 0.0171);Loss of catalytic residue at K115 (P = 0.0171);Loss of catalytic residue at K115 (P = 0.0171);Loss of catalytic residue at K115 (P = 0.0171);
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
No publications associated with this variant yet.