2-215361670-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_212482.4(FN1):c.7363-44C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00105 in 1,426,742 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0052 ( 6 hom., cov: 32)
Exomes 𝑓: 0.00055 ( 5 hom. )
Consequence
FN1
NM_212482.4 intron
NM_212482.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.206
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=-0.63).
BP6
?
Variant 2-215361670-G-A is Benign according to our data. Variant chr2-215361670-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1191771.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00518 (788/152178) while in subpopulation AFR AF= 0.0181 (751/41496). AF 95% confidence interval is 0.017. There are 6 homozygotes in gnomad4. There are 381 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 789 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FN1 | NM_212482.4 | c.7363-44C>T | intron_variant | ENST00000354785.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FN1 | ENST00000354785.11 | c.7363-44C>T | intron_variant | 1 | NM_212482.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00519 AC: 789AN: 152060Hom.: 6 Cov.: 32
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GnomAD3 exomes AF: 0.00142 AC: 354AN: 249148Hom.: 2 AF XY: 0.00111 AC XY: 150AN XY: 135234
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GnomAD4 exome AF: 0.000555 AC: 707AN: 1274564Hom.: 5 Cov.: 19 AF XY: 0.000481 AC XY: 310AN XY: 644162
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GnomAD4 genome ? AF: 0.00518 AC: 788AN: 152178Hom.: 6 Cov.: 32 AF XY: 0.00512 AC XY: 381AN XY: 74422
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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 | GeneDx | Jul 26, 2020 | - - |
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