rs532298569
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3
The NM_020066.5(FMN2):c.665_676delAGCAGCAGCAGC(p.Gln222_Gln225del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,609,564 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
FMN2
NM_020066.5 disruptive_inframe_deletion
NM_020066.5 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.60
Publications
1 publications found
Genes affected
FMN2 (HGNC:14074): (formin 2) This gene is a member of the formin homology protein family. The encoded protein is thought to have essential roles in organization of the actin cytoskeleton and in cell polarity. This protein mediates the formation of an actin mesh that positions the spindle during oogenesis and also regulates the formation of actin filaments in the nucleus. This protein also forms a perinuclear actin/focal-adhesion system that regulates the shape and position of the nucleus during cell migration. Mutations in this gene have been associated with infertility and also with an autosomal recessive form of intellectual disability (MRT47). Alternatively spliced transcript variants have been identified. [provided by RefSeq, Jul 2017]
FMN2 Gene-Disease associations (from GenCC):
- intellectual disability, autosomal recessive 47Inheritance: AR Classification: STRONG Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
- autosomal recessive non-syndromic intellectual disabilityInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_020066.5
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_020066.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| FMN2 | NM_020066.5 | MANE Select | c.665_676delAGCAGCAGCAGC | p.Gln222_Gln225del | disruptive_inframe_deletion | Exon 1 of 18 | NP_064450.3 | ||
| FMN2 | NM_001305424.2 | c.665_676delAGCAGCAGCAGC | p.Gln222_Gln225del | disruptive_inframe_deletion | Exon 1 of 19 | NP_001292353.1 | |||
| FMN2 | NM_001348094.2 | c.665_676delAGCAGCAGCAGC | p.Gln222_Gln225del | disruptive_inframe_deletion | Exon 1 of 15 | NP_001335023.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| FMN2 | ENST00000319653.14 | TSL:5 MANE Select | c.665_676delAGCAGCAGCAGC | p.Gln222_Gln225del | disruptive_inframe_deletion | Exon 1 of 18 | ENSP00000318884.9 | ||
| FMN2 | ENST00000447095.5 | TSL:3 | c.-87+24701_-87+24712delAGCAGCAGCAGC | intron | N/A | ENSP00000409308.1 |
Frequencies
GnomAD3 genomes 0.00000658 AC: 1AN: 151994Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
151994
Hom.:
Cov.:
33
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: 6.86e-7 AC: 1AN: 1457570Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 724938 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1457570
Hom.:
AF XY:
AC XY:
0
AN XY:
724938
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33392
American (AMR)
AF:
AC:
0
AN:
44122
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25986
East Asian (EAS)
AF:
AC:
0
AN:
39626
South Asian (SAS)
AF:
AC:
1
AN:
85960
European-Finnish (FIN)
AF:
AC:
0
AN:
52230
Middle Eastern (MID)
AF:
AC:
0
AN:
5692
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1110382
Other (OTH)
AF:
AC:
0
AN:
60180
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00000658 AC: 1AN: 151994Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74250 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
151994
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
74250
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41416
American (AMR)
AF:
AC:
0
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3464
East Asian (EAS)
AF:
AC:
0
AN:
5166
South Asian (SAS)
AF:
AC:
0
AN:
4824
European-Finnish (FIN)
AF:
AC:
0
AN:
10606
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67932
Other (OTH)
AF:
AC:
0
AN:
2090
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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