22-29674891-C-A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_000268.4(NF2):c.1396C>A(p.Arg466Arg) variant causes a synonymous change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
NF2
NM_000268.4 synonymous
NM_000268.4 synonymous
Scores
3
Clinical Significance
Conservation
PhyloP100: 4.87
Publications
0 publications found
Genes affected
NF2 (HGNC:7773): (NF2, moesin-ezrin-radixin like (MERLIN) tumor suppressor) This gene encodes a protein that is similar to some members of the ERM (ezrin, radixin, moesin) family of proteins that link cytoskeletal components with proteins in the cell membrane. The encoded protein is involved in regulation of contact-dependent inhibition of cell proliferation and functions in cell-cell adhesion and transmembrane signaling. The encoded protein has been shown to interact with cell-surface proteins, proteins involved in cytoskeletal dynamics, and proteins involved in regulating ion transport. Disruption of this protein's function has been implicated in tumorigenesis and metastasis. Mutations in this gene are associated with neurofibromatosis type II which is characterized by nervous system and skin tumors and ocular abnormalities. [provided by RefSeq, May 2022]
NF2 Gene-Disease associations (from GenCC):
- NF2-related schwannomatosisInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
- familial meningiomaInheritance: Unknown Classification: LIMITED Submitted by: Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 22-29674891-C-A is Benign according to our data. Variant chr22-29674891-C-A is described in ClinVar as Likely_benign. ClinVar VariationId is 1771647.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000268.4. 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 |
|---|---|---|---|---|---|---|---|---|---|
| NF2 | MANE Select | c.1396C>A | p.Arg466Arg | synonymous | Exon 13 of 16 | NP_000259.1 | P35240-1 | ||
| NF2 | c.1396C>A | p.Arg466Arg | synonymous | Exon 13 of 17 | NP_001393995.1 | P35240-3 | |||
| NF2 | c.1396C>A | p.Arg466Arg | synonymous | Exon 13 of 17 | NP_057502.2 | P35240-3 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| NF2 | TSL:1 MANE Select | c.1396C>A | p.Arg466Arg | synonymous | Exon 13 of 16 | ENSP00000344666.5 | P35240-1 | ||
| NF2 | TSL:1 | c.1396C>A | p.Arg466Arg | synonymous | Exon 13 of 17 | ENSP00000380891.3 | P35240-3 | ||
| NF2 | TSL:1 | c.1396C>A | p.Arg466Arg | synonymous | Exon 13 of 16 | ENSP00000384797.3 | P35240-3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1422466Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 703622
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1422466
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
703622
African (AFR)
AF:
AC:
0
AN:
32628
American (AMR)
AF:
AC:
0
AN:
39436
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25384
East Asian (EAS)
AF:
AC:
0
AN:
37780
South Asian (SAS)
AF:
AC:
0
AN:
80784
European-Finnish (FIN)
AF:
AC:
0
AN:
50562
Middle Eastern (MID)
AF:
AC:
0
AN:
5728
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1091252
Other (OTH)
AF:
AC:
0
AN:
58912
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
Hereditary cancer-predisposing syndrome (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_noAF
Benign
DANN
Benign
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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