chr8-22046200-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_003867.4(FGF17):c.159C>T(p.Arg53=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000285 in 1,614,070 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00020 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00029 ( 4 hom. )
Consequence
FGF17
NM_003867.4 synonymous
NM_003867.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -6.06
Genes affected
FGF17 (HGNC:3673): (fibroblast growth factor 17) This gene encodes a member of the fibroblast growth factor (FGF) family. Member of the FGF family 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 is expressed during embryogenesis and in the adult cerebellum and cortex and may be essential for vascular growth and normal brain development. Mutations in this gene are the cause of hypogonadotropic hypogonadism 20 with or without anosmia. Alternate 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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BP6
?
Variant 8-22046200-C-T is Benign according to our data. Variant chr8-22046200-C-T is described in ClinVar as [Benign]. Clinvar id is 732853.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-6.06 with no splicing effect.
BS2
?
High AC in GnomAd at 30 AD,Multigenic gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGF17 | NM_003867.4 | c.159C>T | p.Arg53= | synonymous_variant | 3/5 | ENST00000359441.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGF17 | ENST00000359441.4 | c.159C>T | p.Arg53= | synonymous_variant | 3/5 | 1 | NM_003867.4 | P4 | |
FGF17 | ENST00000518533.5 | c.126C>T | p.Arg42= | synonymous_variant | 3/5 | 1 | A1 | ||
FGF17 | ENST00000521709.1 | n.504C>T | non_coding_transcript_exon_variant | 2/3 | 3 | ||||
FGF17 | ENST00000524314.1 | n.1529C>T | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000197 AC: 30AN: 152250Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000438 AC: 110AN: 251338Hom.: 2 AF XY: 0.000434 AC XY: 59AN XY: 135902
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GnomAD4 exome AF: 0.000294 AC: 430AN: 1461702Hom.: 4 Cov.: 33 AF XY: 0.000289 AC XY: 210AN XY: 727160
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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 | Dec 31, 2019 | - - |
Computational 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
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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