rs786203866
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_001042492.3(NF1):c.36C>A(p.Ala12Ala) variant causes a synonymous change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A12A) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
NF1
NM_001042492.3 synonymous
NM_001042492.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.40
Publications
1 publications found
Genes affected
NF1 (HGNC:7765): (neurofibromin 1) This gene product appears to function as a negative regulator of the ras signal transduction pathway. Mutations in this gene have been linked to neurofibromatosis type 1, juvenile myelomonocytic leukemia and Watson syndrome. The mRNA for this gene is subject to RNA editing (CGA>UGA->Arg1306Term) resulting in premature translation termination. Alternatively spliced transcript variants encoding different isoforms have also been described for this gene. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
Variant 17-31095345-C-A is Benign according to our data. Variant chr17-31095345-C-A is described in ClinVar as Likely_benign. ClinVar VariationId is 527624.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| NF1 | NM_001042492.3 | c.36C>A | p.Ala12Ala | synonymous_variant | Exon 1 of 58 | ENST00000358273.9 | NP_001035957.1 | |
| NF1 | NM_000267.4 | c.36C>A | p.Ala12Ala | synonymous_variant | Exon 1 of 57 | NP_000258.1 | ||
| NF1 | NM_001128147.3 | c.36C>A | p.Ala12Ala | synonymous_variant | Exon 1 of 15 | NP_001121619.1 | ||
| MIR4733HG | NR_186435.1 | n.146G>T | non_coding_transcript_exon_variant | Exon 1 of 4 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
30
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1387680Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 684742
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1387680
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
684742
African (AFR)
AF:
AC:
0
AN:
31586
American (AMR)
AF:
AC:
0
AN:
35664
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25124
East Asian (EAS)
AF:
AC:
0
AN:
35860
South Asian (SAS)
AF:
AC:
0
AN:
79138
European-Finnish (FIN)
AF:
AC:
0
AN:
39868
Middle Eastern (MID)
AF:
AC:
0
AN:
4148
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1078548
Other (OTH)
AF:
AC:
0
AN:
57744
GnomAD4 genome
GnomAD4 genome
Cov.:
30
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Neurofibromatosis, type 1 Benign:1
Jul 28, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational 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
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.