chr13-21671954-G-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002010.3(FGF9):c.42G>C(p.Gln14His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000405 in 1,614,194 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0022 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00022 ( 1 hom. )
Consequence
FGF9
NM_002010.3 missense
NM_002010.3 missense
Scores
2
16
Clinical Significance
Conservation
PhyloP100: 2.62
Genes affected
FGF9 (HGNC:3687): (fibroblast growth factor 9) 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 was isolated as a secreted factor that exhibits a growth-stimulating effect on cultured glial cells. In nervous system, this protein is produced mainly by neurons and may be important for glial cell development. Expression of the mouse homolog of this gene was found to be dependent on Sonic hedgehog (Shh) signaling. Mice lacking the homolog gene displayed a male-to-female sex reversal phenotype, which suggested a role in testicular embryogenesis. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.00895375).
BP6
?
Variant 13-21671954-G-C is Benign according to our data. Variant chr13-21671954-G-C is described in ClinVar as [Benign]. Clinvar id is 746291.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 331 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGF9 | NM_002010.3 | c.42G>C | p.Gln14His | missense_variant | 1/3 | ENST00000382353.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGF9 | ENST00000382353.6 | c.42G>C | p.Gln14His | missense_variant | 1/3 | 1 | NM_002010.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00217 AC: 331AN: 152196Hom.: 2 Cov.: 32
GnomAD3 genomes
?
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152196
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32
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GnomAD3 exomes AF: 0.000565 AC: 142AN: 251494Hom.: 0 AF XY: 0.000486 AC XY: 66AN XY: 135920
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GnomAD4 exome AF: 0.000220 AC: 321AN: 1461880Hom.: 1 Cov.: 32 AF XY: 0.000191 AC XY: 139AN XY: 727242
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GnomAD4 genome ? AF: 0.00219 AC: 333AN: 152314Hom.: 2 Cov.: 32 AF XY: 0.00213 AC XY: 159AN XY: 74478
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
P
Vest4
MutPred
Gain of catalytic residue at D15 (P = 0);
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at