rs6725958
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_212482.4(FN1):c.3349-50T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 1,521,204 control chromosomes in the GnomAD database, including 262,996 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.61 ( 28696 hom., cov: 32)
Exomes 𝑓: 0.58 ( 234300 hom. )
Consequence
FN1
NM_212482.4 intron
NM_212482.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.418
Genes affected
FN1 (HGNC:3778): (fibronectin 1) This gene encodes fibronectin, a glycoprotein present in a soluble dimeric form in plasma, and in a dimeric or multimeric form at the cell surface and in extracellular matrix. The encoded preproprotein is proteolytically processed to generate the mature protein. Fibronectin is involved in cell adhesion and migration processes including embryogenesis, wound healing, blood coagulation, host defense, and metastasis. The gene has three regions subject to alternative splicing, with the potential to produce 20 different transcript variants, at least one of which encodes an isoform that undergoes proteolytic processing. The full-length nature of some variants has not been determined. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 2-215397898-A-C is Benign according to our data. Variant chr2-215397898-A-C is described in ClinVar as [Benign]. Clinvar id is 1227605.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FN1 | NM_212482.4 | c.3349-50T>G | intron_variant | ENST00000354785.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FN1 | ENST00000354785.11 | c.3349-50T>G | intron_variant | 1 | NM_212482.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.610 AC: 92648AN: 151964Hom.: 28695 Cov.: 32
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GnomAD3 exomes AF: 0.608 AC: 151758AN: 249656Hom.: 47571 AF XY: 0.596 AC XY: 80457AN XY: 134916
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GnomAD4 exome AF: 0.580 AC: 794673AN: 1369122Hom.: 234300 Cov.: 21 AF XY: 0.576 AC XY: 395013AN XY: 686348
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GnomAD4 genome ? AF: 0.609 AC: 92678AN: 152082Hom.: 28696 Cov.: 32 AF XY: 0.613 AC XY: 45536AN XY: 74342
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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 | GeneDx | Aug 20, 2019 | - - |
Computational 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