chr8-22046518-C-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003867.4(FGF17):c.251-9C>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000634 in 1,608,428 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 0.00017 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000052 ( 0 hom. )
Consequence
FGF17
NM_003867.4 splice_polypyrimidine_tract, intron
NM_003867.4 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.04413
2
Clinical Significance
Conservation
PhyloP100: -0.296
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
?
Variant 8-22046518-C-A is Benign according to our data. Variant chr8-22046518-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 731607.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 25 AD,Multigenic gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGF17 | NM_003867.4 | c.251-9C>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000359441.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGF17 | ENST00000359441.4 | c.251-9C>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_003867.4 | P4 | |||
FGF17 | ENST00000518533.5 | c.218-9C>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | A1 | ||||
FGF17 | ENST00000521709.1 | n.595+227C>A | intron_variant, non_coding_transcript_variant | 3 | |||||
FGF17 | ENST00000524314.1 | n.1621-9C>A | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000164 AC: 25AN: 152242Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000362 AC: 9AN: 248632Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134648
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GnomAD4 exome AF: 0.0000522 AC: 76AN: 1456068Hom.: 0 Cov.: 30 AF XY: 0.0000566 AC XY: 41AN XY: 724432
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 11, 2023 | - - |
Computational scores
Source:
Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at