15-32776687-CTTTTTTTTTT-CTTTTTT
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_001277313.2(FMN1):c.4215+144_4215+147delAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00142 in 452,386 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000082 ( 0 hom., cov: 26)
Exomes 𝑓: 0.0019 ( 0 hom. )
Consequence
FMN1
NM_001277313.2 intron
NM_001277313.2 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.746
Publications
0 publications found
Genes affected
FMN1 (HGNC:3768): (formin 1) This gene belongs to the formin homology family and encodes a protein that has a role in the formation of adherens junction and the polymerization of linear actin cables. The homologous gene in mouse is associated with limb deformity. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2015]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001277313.2. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| FMN1 | NM_001277313.2 | MANE Select | c.4215+144_4215+147delAAAA | intron | N/A | NP_001264242.1 | Q68DA7-1 | ||
| FMN1 | NM_001103184.4 | c.3546+144_3546+147delAAAA | intron | N/A | NP_001096654.1 | Q68DA7-5 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| FMN1 | ENST00000616417.5 | TSL:5 MANE Select | c.4215+144_4215+147delAAAA | intron | N/A | ENSP00000479134.1 | Q68DA7-1 | ||
| FMN1 | ENST00000334528.13 | TSL:1 | c.3546+144_3546+147delAAAA | intron | N/A | ENSP00000333950.9 | Q68DA7-5 | ||
| FMN1 | ENST00000561249.5 | TSL:5 | c.3921+144_3921+147delAAAA | intron | N/A | ENSP00000453443.1 | H0YM30 |
Frequencies
GnomAD3 genomes 0.00000817 AC: 1AN: 122386Hom.: 0 Cov.: 26 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
122386
Hom.:
Cov.:
26
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:
GnomAD4 exome AF: 0.00195 AC: 642AN: 330000Hom.: 0 AF XY: 0.00199 AC XY: 345AN XY: 173630 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
642
AN:
330000
Hom.:
AF XY:
AC XY:
345
AN XY:
173630
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
17
AN:
9000
American (AMR)
AF:
AC:
25
AN:
11020
Ashkenazi Jewish (ASJ)
AF:
AC:
21
AN:
10406
East Asian (EAS)
AF:
AC:
67
AN:
23754
South Asian (SAS)
AF:
AC:
72
AN:
26932
European-Finnish (FIN)
AF:
AC:
39
AN:
23384
Middle Eastern (MID)
AF:
AC:
0
AN:
1976
European-Non Finnish (NFE)
AF:
AC:
367
AN:
204120
Other (OTH)
AF:
AC:
34
AN:
19408
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.250
Heterozygous variant carriers
0
86
171
257
342
428
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
4
8
12
16
20
<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 0.00000817 AC: 1AN: 122386Hom.: 0 Cov.: 26 AF XY: 0.0000170 AC XY: 1AN XY: 58866 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
1
AN:
122386
Hom.:
Cov.:
26
AF XY:
AC XY:
1
AN XY:
58866
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
31462
American (AMR)
AF:
AC:
0
AN:
12314
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2920
East Asian (EAS)
AF:
AC:
0
AN:
4406
South Asian (SAS)
AF:
AC:
0
AN:
3844
European-Finnish (FIN)
AF:
AC:
1
AN:
7000
Middle Eastern (MID)
AF:
AC:
0
AN:
246
European-Non Finnish (NFE)
AF:
AC:
0
AN:
57790
Other (OTH)
AF:
AC:
0
AN:
1590
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.325
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
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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