chr5-177090325-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_213647.3(FGFR4):c.92-65T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 1,597,734 control chromosomes in the GnomAD database, including 515,598 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 0.79 ( 48000 hom., cov: 33)
Exomes 𝑓: 0.80 ( 467598 hom. )
Consequence
FGFR4
NM_213647.3 intron
NM_213647.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.159
Genes affected
FGFR4 (HGNC:3691): (fibroblast growth factor receptor 4) The protein encoded by this gene is a tyrosine kinase and cell surface receptor for fibroblast growth factors. The encoded protein is involved in the regulation of several pathways, including cell proliferation, cell differentiation, cell migration, lipid metabolism, bile acid biosynthesis, vitamin D metabolism, glucose uptake, and phosphate homeostasis. This 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 interacts with fibroblast growth factors, setting in motion a cascade of downstream signals, ultimately influencing mitogenesis and differentiation. [provided by RefSeq, Aug 2017]
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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=-0.92).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGFR4 | NM_213647.3 | c.92-65T>C | intron_variant | ENST00000292408.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGFR4 | ENST00000292408.9 | c.92-65T>C | intron_variant | 1 | NM_213647.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.792 AC: 120426AN: 152042Hom.: 47941 Cov.: 33
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GnomAD3 exomes AF: 0.833 AC: 192963AN: 231708Hom.: 80992 AF XY: 0.833 AC XY: 106193AN XY: 127506
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GnomAD4 exome AF: 0.802 AC: 1159945AN: 1445574Hom.: 467598 Cov.: 38 AF XY: 0.805 AC XY: 579004AN XY: 719554
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GnomAD4 genome ? AF: 0.792 AC: 120544AN: 152160Hom.: 48000 Cov.: 33 AF XY: 0.798 AC XY: 59317AN XY: 74378
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at