rs34003
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000800.5(FGF1):c.274-18T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 1,605,964 control chromosomes in the GnomAD database, including 181,433 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.53 ( 22746 hom., cov: 32)
Exomes 𝑓: 0.46 ( 158687 hom. )
Consequence
FGF1
NM_000800.5 intron
NM_000800.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.132
Genes affected
FGF1 (HGNC:3665): (fibroblast growth factor 1) 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 functions as a modifier of endothelial cell migration and proliferation, as well as an angiogenic factor. It acts as a mitogen for a variety of mesoderm- and neuroectoderm-derived cells in vitro, thus is thought to be involved in organogenesis. Multiple alternatively spliced variants encoding different isoforms have been described. [provided by RefSeq, Jan 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGF1 | NM_000800.5 | c.274-18T>G | intron_variant | ENST00000337706.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGF1 | ENST00000337706.7 | c.274-18T>G | intron_variant | 2 | NM_000800.5 | P1 | |||
SPRY4-AS1 | ENST00000443800.5 | n.356+13588A>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.532 AC: 80852AN: 151882Hom.: 22696 Cov.: 32
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GnomAD3 exomes AF: 0.481 AC: 117529AN: 244134Hom.: 29275 AF XY: 0.479 AC XY: 63329AN XY: 132162
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GnomAD4 exome AF: 0.463 AC: 673165AN: 1453964Hom.: 158687 Cov.: 30 AF XY: 0.463 AC XY: 334957AN XY: 723116
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GnomAD4 genome ? AF: 0.533 AC: 80963AN: 152000Hom.: 22746 Cov.: 32 AF XY: 0.532 AC XY: 39501AN XY: 74282
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at