rs118017785
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_022489.4(INF2):c.843+16C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0748 in 1,555,734 control chromosomes in the GnomAD database, including 4,917 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.059 ( 333 hom., cov: 33)
Exomes 𝑓: 0.076 ( 4584 hom. )
Consequence
INF2
NM_022489.4 intron
NM_022489.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.14
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 14-104706192-C-T is Benign according to our data. Variant chr14-104706192-C-T is described in ClinVar as [Benign]. Clinvar id is 261628.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-104706192-C-T is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0821 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INF2 | NM_022489.4 | c.843+16C>T | intron_variant | ENST00000392634.9 | |||
INF2 | NM_001031714.4 | c.843+16C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INF2 | ENST00000392634.9 | c.843+16C>T | intron_variant | 5 | NM_022489.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0591 AC: 8994AN: 152160Hom.: 333 Cov.: 33
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GnomAD3 exomes AF: 0.0685 AC: 11421AN: 166610Hom.: 489 AF XY: 0.0719 AC XY: 6418AN XY: 89310
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GnomAD4 exome AF: 0.0765 AC: 107317AN: 1403456Hom.: 4584 Cov.: 32 AF XY: 0.0778 AC XY: 53853AN XY: 692062
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GnomAD4 genome ? AF: 0.0590 AC: 8991AN: 152278Hom.: 333 Cov.: 33 AF XY: 0.0573 AC XY: 4270AN XY: 74470
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:4
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 29, 2015 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Focal segmental glomerulosclerosis 5;C4302667:Charcot-Marie-Tooth disease dominant intermediate E Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at