chr5-177092331-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_213647.3(FGFR4):c.738G>A(p.Pro246=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000398 in 1,583,390 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000038 ( 0 hom. )
Consequence
FGFR4
NM_213647.3 synonymous
NM_213647.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.527
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 Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 5-177092331-G-A is Benign according to our data. Variant chr5-177092331-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3056656.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGFR4 | NM_213647.3 | c.738G>A | p.Pro246= | synonymous_variant | 7/18 | ENST00000292408.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGFR4 | ENST00000292408.9 | c.738G>A | p.Pro246= | synonymous_variant | 7/18 | 1 | NM_213647.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152090Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000647 AC: 15AN: 231776Hom.: 0 AF XY: 0.0000636 AC XY: 8AN XY: 125862
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GnomAD4 exome AF: 0.0000384 AC: 55AN: 1431300Hom.: 0 Cov.: 35 AF XY: 0.0000396 AC XY: 28AN XY: 707880
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GnomAD4 genome AF: 0.0000526 AC: 8AN: 152090Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74302
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
FGFR4-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 10, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Benign
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Benign
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Benign
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Details are displayed if max score is > 0.2
DS_AG_spliceai
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at