chr2-215397898-A-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
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
Publications
11 publications found
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]
FN1 Gene-Disease associations (from GenCC):
- spondylometaphyseal dysplasia, 'corner fracture' typeInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, G2P, Ambry Genetics, ClinGen
- glomerulopathy with fibronectin deposits 2Inheritance: AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), ClinGen
- fibronectin glomerulopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -20 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_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.610 AC: 92648AN: 151964Hom.: 28695 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
92648
AN:
151964
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.608 AC: 151758AN: 249656 AF XY: 0.596 show subpopulations
GnomAD2 exomes
AF:
AC:
151758
AN:
249656
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.580 AC: 794673AN: 1369122Hom.: 234300 Cov.: 21 AF XY: 0.576 AC XY: 395013AN XY: 686348 show subpopulations
GnomAD4 exome
AF:
AC:
794673
AN:
1369122
Hom.:
Cov.:
21
AF XY:
AC XY:
395013
AN XY:
686348
show subpopulations
African (AFR)
AF:
AC:
20429
AN:
31562
American (AMR)
AF:
AC:
30577
AN:
44512
Ashkenazi Jewish (ASJ)
AF:
AC:
15238
AN:
25562
East Asian (EAS)
AF:
AC:
37137
AN:
39248
South Asian (SAS)
AF:
AC:
39898
AN:
84342
European-Finnish (FIN)
AF:
AC:
31779
AN:
53174
Middle Eastern (MID)
AF:
AC:
3434
AN:
5558
European-Non Finnish (NFE)
AF:
AC:
582266
AN:
1027812
Other (OTH)
AF:
AC:
33915
AN:
57352
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
16621
33242
49862
66483
83104
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
15934
31868
47802
63736
79670
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.609 AC: 92678AN: 152082Hom.: 28696 Cov.: 32 AF XY: 0.613 AC XY: 45536AN XY: 74342 show subpopulations
GnomAD4 genome
AF:
AC:
92678
AN:
152082
Hom.:
Cov.:
32
AF XY:
AC XY:
45536
AN XY:
74342
show subpopulations
African (AFR)
AF:
AC:
26960
AN:
41472
American (AMR)
AF:
AC:
10042
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
AC:
2100
AN:
3466
East Asian (EAS)
AF:
AC:
4820
AN:
5172
South Asian (SAS)
AF:
AC:
2294
AN:
4822
European-Finnish (FIN)
AF:
AC:
6430
AN:
10578
Middle Eastern (MID)
AF:
AC:
186
AN:
294
European-Non Finnish (NFE)
AF:
AC:
38021
AN:
67980
Other (OTH)
AF:
AC:
1287
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1883
3766
5650
7533
9416
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
758
1516
2274
3032
3790
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2355
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Aug 20, 2019
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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