chr4-80267031-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_004464.4(FGF5):c.207C>T(p.Ser69=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000426 in 1,614,256 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 0.00028 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00044 ( 0 hom. )
Consequence
FGF5
NM_004464.4 synonymous
NM_004464.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.14
Genes affected
FGF5 (HGNC:3683): (fibroblast growth factor 5) 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 gene was identified as an oncogene, which confers transforming potential when transfected into mammalian cells. Targeted disruption of the homolog of this gene in mouse resulted in the phenotype of abnormally long hair, which suggested a function as an inhibitor of hair elongation. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
?
Variant 4-80267031-C-T is Benign according to our data. Variant chr4-80267031-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3045141.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.14 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGF5 | NM_004464.4 | c.207C>T | p.Ser69= | synonymous_variant | 1/3 | ENST00000312465.12 | |
FGF5 | NM_033143.2 | c.207C>T | p.Ser69= | synonymous_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGF5 | ENST00000312465.12 | c.207C>T | p.Ser69= | synonymous_variant | 1/3 | 1 | NM_004464.4 | P1 | |
FGF5 | ENST00000456523.3 | c.207C>T | p.Ser69= | synonymous_variant | 1/2 | 1 | |||
FGF5 | ENST00000380628.3 | n.207C>T | non_coding_transcript_exon_variant | 1/2 | 1 | ||||
FGF5 | ENST00000507780.1 | c.90C>T | p.Ser30= | synonymous_variant, NMD_transcript_variant | 1/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000276 AC: 42AN: 152250Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000179 AC: 45AN: 251448Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135916
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GnomAD4 exome AF: 0.000441 AC: 645AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.000424 AC XY: 308AN XY: 727246
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
FGF5-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 28, 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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Name
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BayesDel_noAF
Benign
Cadd
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Dann
Benign
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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