14-104701371-G-C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_022489.4(INF2):c.6G>C(p.Ser2Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000019 in 1,580,880 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. S2S) has been classified as Benign.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
INF2
NM_022489.4 synonymous
NM_022489.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0960
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: ClinGen, Labcorp Genetics (formerly Invitae), 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: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP7
Synonymous conserved (PhyloP=0.096 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_022489.4. 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.6G>C | p.Ser2Ser | synonymous | Exon 2 of 23 | NP_071934.3 | Q27J81-1 | |
| INF2 | NM_001426862.1 | c.6G>C | p.Ser2Ser | synonymous | Exon 2 of 23 | NP_001413791.1 | |||
| INF2 | NM_001426863.1 | c.6G>C | p.Ser2Ser | synonymous | Exon 2 of 23 | NP_001413792.1 | Q27J81-1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| INF2 | ENST00000392634.9 | TSL:5 MANE Select | c.6G>C | p.Ser2Ser | synonymous | Exon 2 of 23 | ENSP00000376410.4 | Q27J81-1 | |
| INF2 | ENST00000398337.8 | TSL:1 | c.6G>C | p.Ser2Ser | synonymous | Exon 2 of 5 | ENSP00000381380.4 | Q27J81-3 | |
| INF2 | ENST00000617571.5 | TSL:1 | n.6G>C | non_coding_transcript_exon | Exon 1 of 22 | ENSP00000483829.2 | A0A087X118 |
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152246Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
152246
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: 0.00000140 AC: 2AN: 1428634Hom.: 0 Cov.: 31 AF XY: 0.00000141 AC XY: 1AN XY: 707402 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1428634
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
707402
show subpopulations
African (AFR)
AF:
AC:
1
AN:
32738
American (AMR)
AF:
AC:
1
AN:
41544
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25606
East Asian (EAS)
AF:
AC:
0
AN:
37866
South Asian (SAS)
AF:
AC:
0
AN:
82270
European-Finnish (FIN)
AF:
AC:
0
AN:
49728
Middle Eastern (MID)
AF:
AC:
0
AN:
5324
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1094632
Other (OTH)
AF:
AC:
0
AN:
58926
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.450
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
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
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>80
Age
GnomAD4 genome 0.00000657 AC: 1AN: 152246Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74380 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
152246
Hom.:
Cov.:
33
AF XY:
AC XY:
1
AN XY:
74380
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41464
American (AMR)
AF:
AC:
0
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5196
South Asian (SAS)
AF:
AC:
0
AN:
4832
European-Finnish (FIN)
AF:
AC:
0
AN:
10624
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68048
Other (OTH)
AF:
AC:
0
AN:
2090
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
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
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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