chr5-44310216-TG-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_004465.2(FGF10):c.429+210del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00912 in 152,210 control chromosomes in the GnomAD database, including 14 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0091 ( 14 hom., cov: 32)
Consequence
FGF10
NM_004465.2 intron
NM_004465.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.01
Genes affected
FGF10 (HGNC:3666): (fibroblast growth factor 10) 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 protein exhibits mitogenic activity for keratinizing epidermal cells, but essentially no activity for fibroblasts, which is similar to the biological activity of FGF7. Studies of the mouse homolog of suggested that this gene is required for embryonic epidermal morphogenesis including brain development, lung morphogenesis, and initiation of lim bud formation. This gene is also implicated to be a primary factor in the process of wound healing. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 5-44310216-TG-T is Benign according to our data. Variant chr5-44310216-TG-T is described in ClinVar as [Likely_benign]. Clinvar id is 1201459.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00912 (1388/152210) while in subpopulation NFE AF= 0.0127 (867/68008). AF 95% confidence interval is 0.012. There are 14 homozygotes in gnomad4. There are 681 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1388 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FGF10 | NM_004465.2 | c.429+210del | intron_variant | ENST00000264664.5 | NP_004456.1 | |||
FGF10 | XM_005248264.5 | c.429+210del | intron_variant | XP_005248321.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FGF10 | ENST00000264664.5 | c.429+210del | intron_variant | 1 | NM_004465.2 | ENSP00000264664 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00913 AC: 1388AN: 152092Hom.: 14 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.00912 AC: 1388AN: 152210Hom.: 14 Cov.: 32 AF XY: 0.00915 AC XY: 681AN XY: 74404
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3478
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 | GeneDx | Aug 06, 2019 | - - |
Computational scores
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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