rs3829603
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004112.4(FGF11):c.*577A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 152,206 control chromosomes in the GnomAD database, including 36,586 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 0.69 ( 36540 hom., cov: 32)
Exomes 𝑓: 0.80 ( 46 hom. )
Consequence
FGF11
NM_004112.4 3_prime_UTR
NM_004112.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.411
Genes affected
FGF11 (HGNC:3667): (fibroblast growth factor 11) 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. The function of this gene has not yet been determined. The expression pattern of the mouse homolog implies a role in nervous system development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGF11 | NM_004112.4 | c.*577A>C | 3_prime_UTR_variant | 5/5 | ENST00000293829.9 | ||
FGF11 | NM_001303460.2 | c.*577A>C | 3_prime_UTR_variant | 5/5 | |||
FGF11 | NR_130156.2 | n.1295A>C | non_coding_transcript_exon_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGF11 | ENST00000293829.9 | c.*577A>C | 3_prime_UTR_variant | 5/5 | 1 | NM_004112.4 | P1 | ||
FGF11 | ENST00000575082.5 | c.*577A>C | 3_prime_UTR_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.686 AC: 104301AN: 151944Hom.: 36526 Cov.: 32
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GnomAD4 exome AF: 0.796 AC: 113AN: 142Hom.: 46 Cov.: 0 AF XY: 0.829 AC XY: 63AN XY: 76
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GnomAD4 genome ? AF: 0.686 AC: 104362AN: 152064Hom.: 36540 Cov.: 32 AF XY: 0.679 AC XY: 50442AN XY: 74328
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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