rs41538178
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_005247.4(FGF3):c.69G>T(p.Ala23=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 1,460,720 control chromosomes in the GnomAD database, including 8,019 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.098 ( 789 hom., cov: 32)
Exomes 𝑓: 0.10 ( 7230 hom. )
Consequence
FGF3
NM_005247.4 synonymous
NM_005247.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.236
Genes affected
FGF3 (HGNC:3681): (fibroblast growth factor 3) 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 by its similarity with mouse fgf3/int-2, a proto-oncogene activated in virally induced mammary tumors in the mouse. Frequent amplification of this gene has been found in human tumors, which may be important for neoplastic transformation and tumor progression. Studies of the similar genes in mouse and chicken suggested the role in inner ear formation. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
?
Variant 11-69818865-C-A is Benign according to our data. Variant chr11-69818865-C-A is described in ClinVar as [Benign]. Clinvar id is 259690.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.236 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGF3 | NM_005247.4 | c.69G>T | p.Ala23= | synonymous_variant | 1/3 | ENST00000334134.4 | |
LOC107984368 | XR_001748071.2 | n.158C>A | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGF3 | ENST00000334134.4 | c.69G>T | p.Ala23= | synonymous_variant | 1/3 | 1 | NM_005247.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0985 AC: 14943AN: 151716Hom.: 791 Cov.: 32
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GnomAD3 exomes AF: 0.0899 AC: 6822AN: 75870Hom.: 395 AF XY: 0.0913 AC XY: 4024AN XY: 44060
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GnomAD4 exome AF: 0.102 AC: 133292AN: 1308894Hom.: 7230 Cov.: 32 AF XY: 0.102 AC XY: 65743AN XY: 645836
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GnomAD4 genome ? AF: 0.0984 AC: 14946AN: 151826Hom.: 789 Cov.: 32 AF XY: 0.0981 AC XY: 7279AN XY: 74224
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 26, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 10, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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