rs1060499868
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_001426862.1(INF2):c.2019_2022delACAA(p.Lys673AsnfsTer87) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,612,932 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
INF2
NM_001426862.1 frameshift
NM_001426862.1 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.29
Publications
0 publications found
Genes affected
INF2 (HGNC:23791): (inverted formin 2) This gene represents a member of the formin family of proteins. It is considered a diaphanous formin due to the presence of a diaphanous inhibitory domain located at the N-terminus of the encoded protein. Studies of a similar mouse protein indicate that the protein encoded by this locus may function in polymerization and depolymerization of actin filaments. Mutations at this locus have been associated with focal segmental glomerulosclerosis 5.[provided by RefSeq, Aug 2010]
INF2 Gene-Disease associations (from GenCC):
- Charcot-Marie-Tooth disease dominant intermediate EInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Orphanet
- focal segmental glomerulosclerosis 5Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- familial idiopathic steroid-resistant nephrotic syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001426862.1. 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 |
|---|---|---|---|---|---|---|---|---|---|
| INF2 | NM_022489.4 | MANE Select | c.2019_2022delACAA | p.Lys673AsnfsTer87 | frameshift | Exon 11 of 23 | NP_071934.3 | ||
| INF2 | NM_001426862.1 | c.2019_2022delACAA | p.Lys673AsnfsTer87 | frameshift | Exon 11 of 23 | NP_001413791.1 | |||
| INF2 | NM_001426863.1 | c.2019_2022delACAA | p.Lys673AsnfsTer87 | frameshift | Exon 11 of 23 | NP_001413792.1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| INF2 | ENST00000392634.9 | TSL:5 MANE Select | c.2019_2022delACAA | p.Lys673AsnfsTer87 | frameshift | Exon 11 of 23 | ENSP00000376410.4 | ||
| INF2 | ENST00000617571.5 | TSL:1 | n.2019_2022delACAA | non_coding_transcript_exon | Exon 10 of 22 | ENSP00000483829.2 | |||
| INF2 | ENST00000675207.1 | c.2115_2118delACAA | p.Lys705AsnfsTer87 | frameshift | Exon 11 of 23 | ENSP00000502644.1 |
Frequencies
GnomAD3 genomes 0.0000131 AC: 2AN: 152110Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
152110
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
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Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460822Hom.: 0 AF XY: 0.00000275 AC XY: 2AN XY: 726692 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1460822
Hom.:
AF XY:
AC XY:
2
AN XY:
726692
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33480
American (AMR)
AF:
AC:
0
AN:
44710
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39698
South Asian (SAS)
AF:
AC:
0
AN:
86258
European-Finnish (FIN)
AF:
AC:
1
AN:
52612
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1111798
Other (OTH)
AF:
AC:
0
AN:
60362
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
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10
<30
30-35
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>80
Age
GnomAD4 genome 0.0000131 AC: 2AN: 152110Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74302 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
152110
Hom.:
Cov.:
33
AF XY:
AC XY:
1
AN XY:
74302
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41416
American (AMR)
AF:
AC:
0
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5194
South Asian (SAS)
AF:
AC:
0
AN:
4818
European-Finnish (FIN)
AF:
AC:
1
AN:
10622
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
1
AN:
67996
Other (OTH)
AF:
AC:
0
AN:
2088
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational 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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